Starting phenix.real_space_refine on Sat Mar 2 09:20:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fti_4316/03_2024/6fti_4316_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fti_4316/03_2024/6fti_4316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fti_4316/03_2024/6fti_4316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fti_4316/03_2024/6fti_4316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fti_4316/03_2024/6fti_4316_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fti_4316/03_2024/6fti_4316_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 5 6.06 5 P 4012 5.49 5 Mg 159 5.21 5 S 319 5.16 5 C 81289 2.51 5 N 28614 2.21 5 O 39452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G GLU 220": "OE1" <-> "OE2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 4": "NH1" <-> "NH2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ARG 116": "NH1" <-> "NH2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "I ARG 162": "NH1" <-> "NH2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J GLU 93": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "L GLU 142": "OE1" <-> "OE2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M GLU 99": "OE1" <-> "OE2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 119": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M GLU 126": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 131": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 189": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "O ARG 78": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "O GLU 144": "OE1" <-> "OE2" Residue "O GLU 157": "OE1" <-> "OE2" Residue "O GLU 158": "OE1" <-> "OE2" Residue "P GLU 9": "OE1" <-> "OE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 115": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q ARG 37": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q ARG 91": "NH1" <-> "NH2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q ARG 180": "NH1" <-> "NH2" Residue "Q ARG 181": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 42": "NH1" <-> "NH2" Residue "R ARG 74": "NH1" <-> "NH2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 160": "OE1" <-> "OE2" Residue "R ARG 173": "NH1" <-> "NH2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "S ARG 31": "NH1" <-> "NH2" Residue "S ARG 43": "NH1" <-> "NH2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ARG 139": "NH1" <-> "NH2" Residue "T GLU 111": "OE1" <-> "OE2" Residue "T GLU 118": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T GLU 147": "OE1" <-> "OE2" Residue "T GLU 149": "OE1" <-> "OE2" Residue "T GLU 152": "OE1" <-> "OE2" Residue "T GLU 157": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "V ARG 48": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V GLU 71": "OE1" <-> "OE2" Residue "V ARG 89": "NH1" <-> "NH2" Residue "V GLU 99": "OE1" <-> "OE2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "V GLU 124": "OE1" <-> "OE2" Residue "V ARG 131": "NH1" <-> "NH2" Residue "W GLU 4": "OE1" <-> "OE2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Residue "X GLU 91": "OE1" <-> "OE2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "Y ARG 27": "NH1" <-> "NH2" Residue "Y GLU 83": "OE1" <-> "OE2" Residue "Y ARG 87": "NH1" <-> "NH2" Residue "Y GLU 120": "OE1" <-> "OE2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Z ARG 65": "NH1" <-> "NH2" Residue "Z GLU 113": "OE1" <-> "OE2" Residue "Z GLU 119": "OE1" <-> "OE2" Residue "Z GLU 120": "OE1" <-> "OE2" Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ARG 21": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a GLU 84": "OE1" <-> "OE2" Residue "a ARG 105": "NH1" <-> "NH2" Residue "b ARG 14": "NH1" <-> "NH2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b GLU 70": "OE1" <-> "OE2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c GLU 59": "OE1" <-> "OE2" Residue "c GLU 80": "OE1" <-> "OE2" Residue "c TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 19": "OE1" <-> "OE2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "d GLU 124": "OE1" <-> "OE2" Residue "e ARG 36": "NH1" <-> "NH2" Residue "e ARG 39": "NH1" <-> "NH2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "f GLU 38": "OE1" <-> "OE2" Residue "f ARG 89": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h GLU 67": "OE1" <-> "OE2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "h GLU 100": "OE1" <-> "OE2" Residue "h TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 76": "NH1" <-> "NH2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "j ARG 20": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k GLU 6": "OE1" <-> "OE2" Residue "k GLU 54": "OE1" <-> "OE2" Residue "l ARG 28": "NH1" <-> "NH2" Residue "m ARG 97": "NH1" <-> "NH2" Residue "m ARG 111": "NH1" <-> "NH2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "o ARG 40": "NH1" <-> "NH2" Residue "o ARG 43": "NH1" <-> "NH2" Residue "o ARG 78": "NH1" <-> "NH2" Residue "o GLU 92": "OE1" <-> "OE2" Residue "p ARG 17": "NH1" <-> "NH2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "r GLU 28": "OE1" <-> "OE2" Residue "r ARG 35": "NH1" <-> "NH2" Residue "r ARG 46": "NH1" <-> "NH2" Residue "r GLU 52": "OE1" <-> "OE2" Residue "r TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 112": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "r ARG 128": "NH1" <-> "NH2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "s PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 93": "OE1" <-> "OE2" Residue "s GLU 171": "OE1" <-> "OE2" Residue "t GLU 21": "OE1" <-> "OE2" Residue "t GLU 87": "OE1" <-> "OE2" Residue "x ARG 66": "NH1" <-> "NH2" Residue "x PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 405": "NH1" <-> "NH2" Residue "x PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 95": "NH1" <-> "NH2" Residue "1 ARG 458": "NH1" <-> "NH2" Residue "3 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 34": "NH1" <-> "NH2" Residue "5 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 160": "NH1" <-> "NH2" Residue "5 PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 405": "NH1" <-> "NH2" Residue "5 ARG 499": "NH1" <-> "NH2" Residue "5 TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153850 Number of models: 1 Model: "" Number of chains: 76 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1868 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3148 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2884 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2386 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1934 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 226} Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1655 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1703 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "N" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "O" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1506 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1454 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "T" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 808 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "V" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "X" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "c" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "g" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "h" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "l" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "n" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 222 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "r" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1094 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "s" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1523 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "t" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1238 Classifications: {'peptide': 163} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 148} Chain: "q" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1616 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 34} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain breaks: 1 Chain: "u" Number of atoms: 78486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3662, 78486 Classifications: {'DNA': 1, 'RNA': 3661} Modifications used: {'5*END': 1, 'rna2p_pur': 336, 'rna2p_pyr': 220, 'rna3p_pur': 1665, 'rna3p_pyr': 1439} Link IDs: {'rna2p': 556, 'rna3p': 3105} Chain breaks: 12 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' U:plan': 1, ' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 20 Chain: "v" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "w" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 67} Link IDs: {'rna2p': 26, 'rna3p': 129} Chain: "x" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3313 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 408} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "y" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "z" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "1" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 885 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain breaks: 1 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 300 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain breaks: 1 Chain: "3" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 802 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "4" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 268 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "5" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5090 Classifications: {'peptide': 644} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 628} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "6" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Chain breaks: 2 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Chain: "7" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "8" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 400 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'TRANS': 79} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'UNK:plan-1': 80} Unresolved non-hydrogen planarities: 80 Chain: "0" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 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: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 145 Unusual residues: {' MG': 145} Classifications: {'undetermined': 145} Link IDs: {None: 144} Chain: "v" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "w" 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: "5" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'9UB': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 44915 SG CYS g 49 173.059 103.454 72.543 1.00106.89 S ATOM 45178 SG CYS g 83 173.038 106.127 70.158 1.00 82.60 S ATOM 45198 SG CYS g 86 171.258 103.108 69.285 1.00 99.89 S ATOM 47421 SG CYS j 19 127.270 133.725 99.523 1.00 49.01 S ATOM 47449 SG CYS j 22 125.318 134.760 102.068 1.00 73.50 S ATOM 47540 SG CYS j 34 126.084 131.110 102.368 1.00 53.28 S ATOM 47559 SG CYS j 37 123.570 132.962 99.234 1.00 41.74 S ATOM 49161 SG CYS m 96 132.836 84.128 202.978 1.00 66.78 S ATOM 49187 SG CYS m 99 134.755 86.980 202.487 1.00 76.03 S ATOM 49277 SG CYS m 110 133.108 86.689 205.642 1.00 62.24 S ATOM 49321 SG CYS m 115 131.312 87.282 202.673 1.00 80.82 S ATOM 49741 SG CYS o 12 59.113 70.525 120.067 1.00 98.29 S ATOM 49765 SG CYS o 15 56.222 69.326 118.442 1.00 89.96 S ATOM 50234 SG CYS o 72 60.154 67.654 118.787 1.00 94.48 S ATOM 50271 SG CYS o 77 59.208 70.075 116.404 1.00116.98 S ATOM 50801 SG CYS p 39 172.188 89.765 78.332 1.00 76.03 S ATOM 50824 SG CYS p 42 176.123 90.271 77.717 1.00 78.46 S ATOM 50946 SG CYS p 57 173.135 92.214 79.986 1.00 65.95 S ATOM 50962 SG CYS p 60 173.253 91.487 78.077 1.00 71.15 S Time building chain proxies: 57.26, per 1000 atoms: 0.37 Number of scatterers: 153850 At special positions: 0 Unit cell: (244.442, 295.715, 273.06, 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 5 29.99 S 319 16.00 P 4012 15.00 Mg 159 11.99 O 39452 8.00 N 28614 7.00 C 81289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 97355 O5' G u2433 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=5, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG K 1 " - " ASN 5 548 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.30 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " Number of angles added : 24 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16024 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: 304 helices and 67 sheets defined 48.9% alpha, 11.6% beta 1230 base pairs and 1953 stacking pairs defined. Time for finding SS restraints: 80.12 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 6.492A pdb=" N LYS A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.505A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 4.081A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.643A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 173 through 178 Proline residue: A 178 - end of helix Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.299A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.909A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 157 Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.293A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Proline residue: B 172 - end of helix No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.901A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.360A pdb=" N LYS C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 33 through 49 removed outlier: 3.529A pdb=" N PHE C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 134 removed outlier: 3.522A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 135 through 141 Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.730A pdb=" N GLY C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.794A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 4.524A pdb=" N MET C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 198' Processing helix chain 'C' and resid 216 through 223 removed outlier: 4.287A pdb=" N ARG C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASN C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 242 Proline residue: C 242 - end of helix Processing helix chain 'C' and resid 253 through 264 removed outlier: 5.083A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.531A pdb=" N ILE C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 4.166A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.103A pdb=" N LEU C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 330 through 363 removed outlier: 4.536A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 removed outlier: 5.876A pdb=" N GLN C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER C 63 " --> pdb=" O HIS C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 63' Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.868A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.303A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 removed outlier: 3.503A pdb=" N ARG D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.755A pdb=" N TYR D 119 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 115 through 120' Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 191 through 201 removed outlier: 6.392A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.526A pdb=" N TYR D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.842A pdb=" N SER D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 removed outlier: 4.257A pdb=" N ASN D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 230' Processing helix chain 'D' and resid 232 through 250 removed outlier: 4.749A pdb=" N GLU D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 294 removed outlier: 4.775A pdb=" N ARG D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 removed outlier: 4.297A pdb=" N MET E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.670A pdb=" N HIS E 132 " --> pdb=" O PRO E 128 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL E 133 " --> pdb=" O PHE E 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 128 through 133' Processing helix chain 'E' and resid 186 through 191 removed outlier: 3.884A pdb=" N VAL E 190 " --> pdb=" O HIS E 186 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 191' Processing helix chain 'E' and resid 209 through 214 removed outlier: 3.972A pdb=" N LYS E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 258 removed outlier: 3.620A pdb=" N LYS E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 262 through 270 removed outlier: 5.238A pdb=" N VAL E 270 " --> pdb=" O TYR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 5.044A pdb=" N VAL E 283 " --> pdb=" O PRO E 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 81 removed outlier: 4.013A pdb=" N MET F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 80 " --> pdb=" O MET F 76 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 128 through 139 Processing helix chain 'F' and resid 148 through 158 removed outlier: 3.550A pdb=" N VAL F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 181 removed outlier: 3.851A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 199 Processing helix chain 'F' and resid 202 through 211 removed outlier: 5.199A pdb=" N TRP F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.657A pdb=" N LEU F 245 " --> pdb=" O GLN F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.608A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU G 70 " --> pdb=" O GLN G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 4.982A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.907A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 123 removed outlier: 6.181A pdb=" N LYS G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG G 117 " --> pdb=" O ARG G 113 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 150 removed outlier: 3.548A pdb=" N LEU G 146 " --> pdb=" O THR G 142 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 178 Proline residue: G 171 - end of helix Processing helix chain 'G' and resid 186 through 195 removed outlier: 3.920A pdb=" N LEU G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 226 removed outlier: 3.681A pdb=" N ASN G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'G' and resid 243 through 265 removed outlier: 3.549A pdb=" N ARG G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU G 265 " --> pdb=" O LEU G 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 86 removed outlier: 4.290A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 4.399A pdb=" N THR H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.063A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 10 removed outlier: 4.498A pdb=" N TYR I 9 " --> pdb=" O PRO I 5 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 5 through 10' Processing helix chain 'I' and resid 42 through 47 removed outlier: 3.870A pdb=" N PHE I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix No H-bonds generated for 'chain 'I' and resid 42 through 47' Processing helix chain 'I' and resid 61 through 80 Processing helix chain 'I' and resid 144 through 160 removed outlier: 3.954A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 177 through 188 removed outlier: 4.704A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 214 removed outlier: 3.956A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS I 213 " --> pdb=" O TRP I 209 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER I 214 " --> pdb=" O ARG I 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 45 removed outlier: 3.558A pdb=" N THR J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS J 38 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL J 39 " --> pdb=" O ARG J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 111 through 116 removed outlier: 4.397A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY J 116 " --> pdb=" O HIS J 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 116' Processing helix chain 'J' and resid 139 through 144 removed outlier: 4.688A pdb=" N ASP J 143 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 157 removed outlier: 5.885A pdb=" N ARG J 156 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE J 157 " --> pdb=" O ALA J 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 157' Processing helix chain 'J' and resid 158 through 169 Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.069A pdb=" N ARG L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.933A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 87 through 95 removed outlier: 3.766A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY L 95 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 124 removed outlier: 3.606A pdb=" N LEU L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 146 removed outlier: 3.958A pdb=" N GLU L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 177 removed outlier: 5.487A pdb=" N ASN L 175 " --> pdb=" O GLU L 171 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 192 removed outlier: 3.536A pdb=" N ALA L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 211 removed outlier: 3.709A pdb=" N LYS L 210 " --> pdb=" O ASP L 206 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS L 211 " --> pdb=" O VAL L 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 56 removed outlier: 3.868A pdb=" N MET M 55 " --> pdb=" O PRO M 51 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLN M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 51 through 56' Processing helix chain 'M' and resid 69 through 81 removed outlier: 5.896A pdb=" N VAL M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 removed outlier: 5.547A pdb=" N ARG M 90 " --> pdb=" O TRP M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 removed outlier: 3.533A pdb=" N ARG M 98 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET M 104 " --> pdb=" O ARG M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 139 Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.781A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.851A pdb=" N LEU N 33 " --> pdb=" O GLN N 29 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 83 through 88 removed outlier: 3.839A pdb=" N HIS N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLY N 88 " --> pdb=" O PRO N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 88' Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.735A pdb=" N GLY N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 145 removed outlier: 3.689A pdb=" N ASN N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 153 removed outlier: 4.408A pdb=" N TRP N 150 " --> pdb=" O PRO N 146 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE N 151 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR N 152 " --> pdb=" O THR N 148 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS N 153 " --> pdb=" O GLN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 146 through 153' Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.650A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY N 173 " --> pdb=" O ARG N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 185 removed outlier: 6.395A pdb=" N ILE N 184 " --> pdb=" O PHE N 180 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY N 185 " --> pdb=" O HIS N 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 180 through 185' Processing helix chain 'N' and resid 187 through 197 Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.685A pdb=" N ILE O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY O 30 " --> pdb=" O GLN O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.873A pdb=" N ILE O 41 " --> pdb=" O ARG O 37 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASN O 42 " --> pdb=" O CYS O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 42' Processing helix chain 'O' and resid 46 through 61 removed outlier: 3.554A pdb=" N ASN O 50 " --> pdb=" O ASN O 46 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.735A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.851A pdb=" N MET O 87 " --> pdb=" O THR O 83 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 92 through 103 removed outlier: 3.544A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 4.534A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 150 through 190 removed outlier: 3.596A pdb=" N LYS O 159 " --> pdb=" O THR O 155 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS O 167 " --> pdb=" O LYS O 163 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS O 183 " --> pdb=" O LYS O 179 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS O 188 " --> pdb=" O ASN O 184 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP O 190 " --> pdb=" O GLU O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 200 removed outlier: 4.766A pdb=" N VAL O 195 " --> pdb=" O ARG O 191 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS O 197 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS O 199 " --> pdb=" O VAL O 195 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY O 200 " --> pdb=" O LEU O 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 15 removed outlier: 3.925A pdb=" N SER P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N CYS P 15 " --> pdb=" O PRO P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 10 through 15' Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.258A pdb=" N LYS P 74 " --> pdb=" O CYS P 70 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLN P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.569A pdb=" N HIS P 93 " --> pdb=" O GLU P 89 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET P 94 " --> pdb=" O PHE P 90 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 54 removed outlier: 3.908A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE Q 52 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N SER Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 Processing helix chain 'Q' and resid 106 through 117 removed outlier: 3.573A pdb=" N GLY Q 117 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 146 through 153 removed outlier: 4.487A pdb=" N ARG Q 150 " --> pdb=" O ARG Q 146 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS Q 151 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY Q 153 " --> pdb=" O TYR Q 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 146 through 153' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 6.296A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 4.137A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 5.832A pdb=" N ARG R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.492A pdb=" N VAL R 93 " --> pdb=" O MET R 89 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG R 104 " --> pdb=" O ARG R 100 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS R 113 " --> pdb=" O TYR R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 removed outlier: 3.642A pdb=" N ASN R 130 " --> pdb=" O LYS R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 181 removed outlier: 3.761A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 117 Processing helix chain 'S' and resid 120 through 125 removed outlier: 3.788A pdb=" N ILE S 124 " --> pdb=" O ARG S 120 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN S 125 " --> pdb=" O ALA S 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 120 through 125' Processing helix chain 'S' and resid 139 through 147 removed outlier: 5.071A pdb=" N PHE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS S 146 " --> pdb=" O VAL S 142 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP S 147 " --> pdb=" O LYS S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 166 Proline residue: S 165 - end of helix No H-bonds generated for 'chain 'S' and resid 161 through 166' Processing helix chain 'T' and resid 11 through 16 removed outlier: 4.856A pdb=" N SER T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.756A pdb=" N TYR T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 59 removed outlier: 3.678A pdb=" N HIS T 58 " --> pdb=" O HIS T 54 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY T 59 " --> pdb=" O LYS T 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 54 through 59' Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.603A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LYS T 97 " --> pdb=" O ILE T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 100 through 123 removed outlier: 3.660A pdb=" N SER T 104 " --> pdb=" O LYS T 100 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE T 105 " --> pdb=" O SER T 101 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU T 121 " --> pdb=" O LYS T 117 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS T 122 " --> pdb=" O GLU T 118 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY T 123 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.906A pdb=" N VAL U 29 " --> pdb=" O CYS U 25 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP U 31 " --> pdb=" O HIS U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 55 through 60 removed outlier: 4.798A pdb=" N GLY U 59 " --> pdb=" O ASN U 55 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL U 60 " --> pdb=" O LEU U 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 55 through 60' Processing helix chain 'U' and resid 79 through 95 removed outlier: 4.486A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 74 removed outlier: 5.821A pdb=" N LYS V 74 " --> pdb=" O PRO V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 129 removed outlier: 3.799A pdb=" N LEU V 128 " --> pdb=" O GLU V 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 136 Processing helix chain 'W' and resid 33 through 43 removed outlier: 3.503A pdb=" N ALA W 39 " --> pdb=" O LYS W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 50 removed outlier: 3.839A pdb=" N ILE W 49 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 45 through 50' Processing helix chain 'W' and resid 52 through 60 Processing helix chain 'X' and resid 72 through 78 removed outlier: 4.004A pdb=" N ILE X 77 " --> pdb=" O HIS X 73 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS X 78 " --> pdb=" O TYR X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 93 Processing helix chain 'X' and resid 105 through 118 Processing helix chain 'X' and resid 145 through 154 Processing helix chain 'Y' and resid 10 through 21 removed outlier: 3.544A pdb=" N ALA Y 21 " --> pdb=" O ARG Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 31 removed outlier: 3.974A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER Y 31 " --> pdb=" O ARG Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 4.294A pdb=" N VAL Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 134 Processing helix chain 'Z' and resid 58 through 67 removed outlier: 4.555A pdb=" N ILE Z 62 " --> pdb=" O GLY Z 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.860A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N MET Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 4.035A pdb=" N ASN Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 104 removed outlier: 4.851A pdb=" N ARG Z 102 " --> pdb=" O LYS Z 98 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP Z 103 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) Proline residue: Z 104 - end of helix No H-bonds generated for 'chain 'Z' and resid 98 through 104' Processing helix chain 'Z' and resid 105 through 125 removed outlier: 4.829A pdb=" N THR Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 3.801A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN Z 132 " --> pdb=" O LYS Z 128 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 127 through 133' Processing helix chain 'a' and resid 2 through 7 removed outlier: 5.279A pdb=" N LYS a 7 " --> pdb=" O SER a 3 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 64 through 69 removed outlier: 4.462A pdb=" N SER a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE a 69 " --> pdb=" O ARG a 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 64 through 69' Processing helix chain 'a' and resid 74 through 83 removed outlier: 3.652A pdb=" N LEU a 78 " --> pdb=" O ASN a 74 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER a 83 " --> pdb=" O TRP a 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 74 through 83' Processing helix chain 'a' and resid 84 through 93 removed outlier: 4.137A pdb=" N ALA a 90 " --> pdb=" O THR a 86 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA a 91 " --> pdb=" O ARG a 87 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS a 92 " --> pdb=" O VAL a 88 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASN a 93 " --> pdb=" O ASN a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 107 removed outlier: 3.827A pdb=" N SER a 106 " --> pdb=" O ASP a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 141 Processing helix chain 'b' and resid 11 through 20 removed outlier: 4.483A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY b 20 " --> pdb=" O TRP b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 55 removed outlier: 5.069A pdb=" N LYS b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY b 53 " --> pdb=" O HIS b 49 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU b 54 " --> pdb=" O ASN b 50 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 76 Processing helix chain 'c' and resid 13 through 24 removed outlier: 4.017A pdb=" N ARG c 17 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU c 20 " --> pdb=" O SER c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 41 removed outlier: 3.816A pdb=" N LYS c 36 " --> pdb=" O LYS c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 Processing helix chain 'd' and resid 28 through 34 removed outlier: 4.167A pdb=" N ARG d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 37 through 57 removed outlier: 5.275A pdb=" N ALA d 42 " --> pdb=" O PHE d 38 " (cutoff:3.500A) Proline residue: d 43 - end of helix removed outlier: 3.518A pdb=" N LEU d 46 " --> pdb=" O ALA d 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'e' and resid 24 through 29 removed outlier: 3.560A pdb=" N TYR e 28 " --> pdb=" O GLN e 24 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL e 29 " --> pdb=" O SER e 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 24 through 29' Processing helix chain 'e' and resid 43 through 48 Processing helix chain 'e' and resid 57 through 62 removed outlier: 4.449A pdb=" N GLY e 61 " --> pdb=" O ASN e 57 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER e 62 " --> pdb=" O ILE e 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 57 through 62' Processing helix chain 'e' and resid 81 through 90 removed outlier: 3.577A pdb=" N LEU e 85 " --> pdb=" O ASN e 81 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU e 86 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU e 88 " --> pdb=" O GLU e 84 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU e 89 " --> pdb=" O LEU e 85 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N MET e 90 " --> pdb=" O GLU e 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 81 through 90' Processing helix chain 'e' and resid 104 through 119 removed outlier: 4.044A pdb=" N LYS e 109 " --> pdb=" O SER e 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 40 removed outlier: 3.810A pdb=" N THR f 39 " --> pdb=" O ALA f 35 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU f 40 " --> pdb=" O ARG f 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 35 through 40' Processing helix chain 'f' and resid 93 through 98 removed outlier: 6.799A pdb=" N ILE f 97 " --> pdb=" O PRO f 93 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY f 98 " --> pdb=" O ALA f 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 93 through 98' Processing helix chain 'g' and resid 60 through 67 removed outlier: 4.005A pdb=" N LEU g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET g 65 " --> pdb=" O PRO g 61 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG g 66 " --> pdb=" O LYS g 62 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 60 through 67' Processing helix chain 'g' and resid 68 through 73 Processing helix chain 'g' and resid 83 through 115 removed outlier: 3.567A pdb=" N LYS g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU g 98 " --> pdb=" O ALA g 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.076A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 Processing helix chain 'h' and resid 40 through 74 removed outlier: 4.230A pdb=" N LYS h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 85 Proline residue: h 85 - end of helix Processing helix chain 'h' and resid 88 through 95 removed outlier: 3.757A pdb=" N ARG h 93 " --> pdb=" O ARG h 89 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU h 95 " --> pdb=" O MET h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 102 removed outlier: 6.473A pdb=" N GLU h 100 " --> pdb=" O ASN h 96 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER h 101 " --> pdb=" O LYS h 97 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU h 102 " --> pdb=" O HIS h 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 96 through 102' Processing helix chain 'h' and resid 104 through 114 Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.359A pdb=" N ARG i 29 " --> pdb=" O ARG i 25 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG i 30 " --> pdb=" O HIS i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.505A pdb=" N GLU i 46 " --> pdb=" O ASP i 42 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL i 47 " --> pdb=" O MET i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 103 removed outlier: 4.737A pdb=" N LYS i 103 " --> pdb=" O LYS i 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.606A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.940A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 4.312A pdb=" N ILE j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.669A pdb=" N ARG k 17 " --> pdb=" O LEU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 60 removed outlier: 3.968A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU k 60 " --> pdb=" O LEU k 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.561A pdb=" N ASN l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG l 21 " --> pdb=" O GLN l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.174A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.585A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 24 removed outlier: 3.865A pdb=" N ARG n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER n 24 " --> pdb=" O MET n 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 47 removed outlier: 5.877A pdb=" N GLY o 47 " --> pdb=" O ARG o 43 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.873A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'r' and resid 2 through 11 removed outlier: 3.973A pdb=" N GLN r 6 " --> pdb=" O SER r 2 " (cutoff:3.500A) Processing helix chain 'r' and resid 72 through 77 removed outlier: 4.217A pdb=" N TYR r 77 " --> pdb=" O PRO r 73 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 98 removed outlier: 4.391A pdb=" N THR r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 123 removed outlier: 3.723A pdb=" N ALA r 110 " --> pdb=" O LEU r 106 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS r 122 " --> pdb=" O LEU r 118 " (cutoff:3.500A) Proline residue: r 123 - end of helix Processing helix chain 'r' and resid 124 through 133 removed outlier: 3.822A pdb=" N ARG r 132 " --> pdb=" O ARG r 128 " (cutoff:3.500A) Proline residue: r 133 - end of helix Processing helix chain 's' and resid 5 through 24 removed outlier: 6.072A pdb=" N TRP s 9 " --> pdb=" O ASP s 5 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) Processing helix chain 's' and resid 36 through 48 Processing helix chain 's' and resid 57 through 71 removed outlier: 3.853A pdb=" N MET s 61 " --> pdb=" O LYS s 57 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ARG s 62 " --> pdb=" O ASN s 58 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS s 63 " --> pdb=" O THR s 59 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA s 64 " --> pdb=" O MET s 60 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE s 65 " --> pdb=" O MET s 61 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU s 70 " --> pdb=" O ARG s 66 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN s 71 " --> pdb=" O GLY s 67 " (cutoff:3.500A) Processing helix chain 's' and resid 74 through 79 removed outlier: 4.296A pdb=" N LEU s 78 " --> pdb=" O ALA s 74 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU s 79 " --> pdb=" O LEU s 75 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 74 through 79' Processing helix chain 's' and resid 94 through 106 removed outlier: 4.650A pdb=" N ILE s 98 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS s 106 " --> pdb=" O LEU s 102 " (cutoff:3.500A) Processing helix chain 's' and resid 134 through 142 removed outlier: 4.844A pdb=" N PHE s 138 " --> pdb=" O LYS s 134 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU s 141 " --> pdb=" O PHE s 137 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY s 142 " --> pdb=" O PHE s 138 " (cutoff:3.500A) Processing helix chain 's' and resid 168 through 179 Processing helix chain 't' and resid 31 through 37 removed outlier: 5.021A pdb=" N LEU t 35 " --> pdb=" O LYS t 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY t 36 " --> pdb=" O ILE t 32 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU t 37 " --> pdb=" O GLY t 33 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 31 through 37' Processing helix chain 't' and resid 40 through 52 Processing helix chain 't' and resid 77 through 87 removed outlier: 5.698A pdb=" N GLU t 87 " --> pdb=" O LYS t 83 " (cutoff:3.500A) Processing helix chain 't' and resid 107 through 117 removed outlier: 4.267A pdb=" N ASN t 111 " --> pdb=" O ASP t 107 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE t 112 " --> pdb=" O GLU t 108 " (cutoff:3.500A) Processing helix chain 't' and resid 125 through 137 removed outlier: 3.679A pdb=" N ILE t 129 " --> pdb=" O LEU t 125 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU t 131 " --> pdb=" O GLY t 127 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR t 135 " --> pdb=" O GLU t 131 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN t 137 " --> pdb=" O LEU t 133 " (cutoff:3.500A) Processing helix chain 't' and resid 150 through 155 removed outlier: 4.526A pdb=" N ASP t 154 " --> pdb=" O ASP t 150 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE t 155 " --> pdb=" O ILE t 151 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 150 through 155' Processing helix chain 't' and resid 93 through 98 removed outlier: 6.312A pdb=" N LYS t 96 " --> pdb=" O LYS t 93 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASN t 97 " --> pdb=" O LYS t 94 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE t 98 " --> pdb=" O GLN t 95 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 93 through 98' Processing helix chain 'x' and resid 5 through 14 removed outlier: 6.031A pdb=" N ILE x 9 " --> pdb=" O PHE x 5 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Proline residue: x 11 - end of helix removed outlier: 4.884A pdb=" N VAL x 14 " --> pdb=" O LYS x 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 5 through 14' Processing helix chain 'x' and resid 27 through 47 removed outlier: 5.328A pdb=" N LYS x 31 " --> pdb=" O GLN x 27 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL x 32 " --> pdb=" O PHE x 28 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR x 38 " --> pdb=" O TRP x 34 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS x 46 " --> pdb=" O PHE x 42 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN x 47 " --> pdb=" O LEU x 43 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 69 Processing helix chain 'x' and resid 81 through 98 removed outlier: 3.540A pdb=" N MET x 91 " --> pdb=" O SER x 87 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS x 98 " --> pdb=" O LEU x 94 " (cutoff:3.500A) Processing helix chain 'x' and resid 105 through 133 Processing helix chain 'x' and resid 150 through 172 removed outlier: 3.831A pdb=" N VAL x 162 " --> pdb=" O ALA x 158 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS x 171 " --> pdb=" O GLU x 167 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY x 172 " --> pdb=" O LEU x 168 " (cutoff:3.500A) Processing helix chain 'x' and resid 177 through 197 removed outlier: 4.608A pdb=" N LEU x 181 " --> pdb=" O SER x 177 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS x 194 " --> pdb=" O THR x 190 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER x 197 " --> pdb=" O TRP x 193 " (cutoff:3.500A) Processing helix chain 'x' and resid 212 through 223 removed outlier: 5.052A pdb=" N LEU x 220 " --> pdb=" O LEU x 216 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA x 221 " --> pdb=" O PHE x 217 " (cutoff:3.500A) Processing helix chain 'x' and resid 225 through 235 removed outlier: 3.975A pdb=" N GLU x 232 " --> pdb=" O ARG x 228 " (cutoff:3.500A) Processing helix chain 'x' and resid 241 through 262 removed outlier: 3.801A pdb=" N GLY x 260 " --> pdb=" O ILE x 256 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE x 261 " --> pdb=" O TYR x 257 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG x 262 " --> pdb=" O PHE x 258 " (cutoff:3.500A) Processing helix chain 'x' and resid 291 through 312 removed outlier: 3.979A pdb=" N VAL x 298 " --> pdb=" O GLN x 294 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER x 299 " --> pdb=" O SER x 295 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL x 303 " --> pdb=" O SER x 299 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N MET x 307 " --> pdb=" O VAL x 303 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU x 308 " --> pdb=" O ILE x 304 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER x 309 " --> pdb=" O SER x 305 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG x 311 " --> pdb=" O MET x 307 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE x 312 " --> pdb=" O LEU x 308 " (cutoff:3.500A) Processing helix chain 'x' and resid 339 through 346 removed outlier: 3.867A pdb=" N HIS x 343 " --> pdb=" O GLY x 339 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR x 344 " --> pdb=" O GLY x 340 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU x 345 " --> pdb=" O LEU x 341 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER x 346 " --> pdb=" O CYS x 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 339 through 346' Processing helix chain 'x' and resid 357 through 383 removed outlier: 3.711A pdb=" N ALA x 361 " --> pdb=" O ASP x 357 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU x 381 " --> pdb=" O LYS x 377 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL x 382 " --> pdb=" O THR x 378 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER x 383 " --> pdb=" O TRP x 379 " (cutoff:3.500A) Processing helix chain 'x' and resid 386 through 398 Processing helix chain 'x' and resid 406 through 439 removed outlier: 4.795A pdb=" N VAL x 410 " --> pdb=" O GLU x 406 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N HIS x 411 " --> pdb=" O THR x 407 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG x 415 " --> pdb=" O HIS x 411 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR x 416 " --> pdb=" O GLU x 412 " (cutoff:3.500A) Proline residue: x 418 - end of helix removed outlier: 4.021A pdb=" N GLY x 424 " --> pdb=" O ALA x 420 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE x 428 " --> pdb=" O GLY x 424 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY x 429 " --> pdb=" O GLY x 425 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU x 431 " --> pdb=" O CYS x 427 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU x 438 " --> pdb=" O LEU x 434 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY x 439 " --> pdb=" O ALA x 435 " (cutoff:3.500A) Processing helix chain 'x' and resid 444 through 465 removed outlier: 3.619A pdb=" N LEU x 448 " --> pdb=" O GLY x 444 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU x 464 " --> pdb=" O ILE x 460 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN x 465 " --> pdb=" O PHE x 461 " (cutoff:3.500A) Processing helix chain 'y' and resid 8 through 25 removed outlier: 3.839A pdb=" N ARG y 12 " --> pdb=" O VAL y 8 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE y 19 " --> pdb=" O VAL y 15 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU y 21 " --> pdb=" O ASP y 17 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS y 23 " --> pdb=" O ILE y 19 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG y 24 " --> pdb=" O ARG y 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) Processing helix chain 'y' and resid 29 through 68 removed outlier: 3.539A pdb=" N PHE y 33 " --> pdb=" O ASP y 29 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN y 34 " --> pdb=" O ARG y 30 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE y 50 " --> pdb=" O ILE y 46 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLY y 51 " --> pdb=" O MET y 47 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE y 52 " --> pdb=" O GLY y 48 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE y 59 " --> pdb=" O LYS y 55 " (cutoff:3.500A) Proline residue: y 60 - end of helix Processing helix chain 'z' and resid 71 through 96 removed outlier: 3.683A pdb=" N ILE z 89 " --> pdb=" O PHE z 85 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY z 91 " --> pdb=" O LEU z 87 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS z 92 " --> pdb=" O HIS z 88 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR z 94 " --> pdb=" O TRP z 90 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG z 95 " --> pdb=" O GLY z 91 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER z 96 " --> pdb=" O LYS z 92 " (cutoff:3.500A) Processing helix chain '1' and resid 438 through 459 Processing helix chain '1' and resid 466 through 505 removed outlier: 4.294A pdb=" N ALA 1 473 " --> pdb=" O ALA 1 469 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA 1 502 " --> pdb=" O ALA 1 498 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA 1 503 " --> pdb=" O ALA 1 499 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA 1 504 " --> pdb=" O ALA 1 500 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA 1 505 " --> pdb=" O ALA 1 501 " (cutoff:3.500A) Processing helix chain '1' and resid 509 through 539 removed outlier: 4.254A pdb=" N ALA 1 538 " --> pdb=" O ALA 1 534 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA 1 539 " --> pdb=" O ALA 1 535 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 573 Processing helix chain '1' and resid 582 through 606 Processing helix chain '2' and resid 17 through 41 Processing helix chain '2' and resid 50 through 75 removed outlier: 4.915A pdb=" N ALA 2 55 " --> pdb=" O ALA 2 51 " (cutoff:3.500A) Processing helix chain '3' and resid 30 through 54 removed outlier: 3.836A pdb=" N TYR 3 34 " --> pdb=" O ALA 3 30 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE 3 42 " --> pdb=" O VAL 3 38 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 3 43 " --> pdb=" O VAL 3 39 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY 3 47 " --> pdb=" O LEU 3 43 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE 3 48 " --> pdb=" O ILE 3 44 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE 3 49 " --> pdb=" O THR 3 45 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR 3 50 " --> pdb=" O GLY 3 46 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL 3 52 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE 3 53 " --> pdb=" O ILE 3 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL 3 54 " --> pdb=" O TYR 3 50 " (cutoff:3.500A) Processing helix chain '3' and resid 83 through 111 removed outlier: 3.653A pdb=" N ALA 3 89 " --> pdb=" O MET 3 85 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY 3 97 " --> pdb=" O LEU 3 93 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA 3 109 " --> pdb=" O ASP 3 105 " (cutoff:3.500A) Proline residue: 3 110 - end of helix Processing helix chain '3' and resid 116 through 145 removed outlier: 4.374A pdb=" N LEU 3 120 " --> pdb=" O ASN 3 116 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU 3 121 " --> pdb=" O ARG 3 117 " (cutoff:3.500A) Proline residue: 3 144 - end of helix Processing helix chain '4' and resid 3 through 32 removed outlier: 3.512A pdb=" N ASN 4 32 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 41 removed outlier: 4.457A pdb=" N THR 5 16 " --> pdb=" O GLU 5 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU 5 21 " --> pdb=" O LEU 5 17 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA 5 27 " --> pdb=" O LEU 5 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 5 30 " --> pdb=" O ALA 5 26 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE 5 31 " --> pdb=" O ALA 5 27 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU 5 35 " --> pdb=" O PHE 5 31 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE 5 36 " --> pdb=" O SER 5 32 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL 5 38 " --> pdb=" O ARG 5 34 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE 5 41 " --> pdb=" O ALA 5 37 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 63 removed outlier: 5.061A pdb=" N TYR 5 51 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE 5 52 " --> pdb=" O PHE 5 48 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN 5 53 " --> pdb=" O ASP 5 49 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR 5 56 " --> pdb=" O PHE 5 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA 5 61 " --> pdb=" O THR 5 57 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 88 removed outlier: 5.152A pdb=" N THR 5 87 " --> pdb=" O ILE 5 83 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU 5 88 " --> pdb=" O ILE 5 84 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 83 through 88' Processing helix chain '5' and resid 90 through 107 removed outlier: 4.444A pdb=" N HIS 5 104 " --> pdb=" O TYR 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 111 through 139 removed outlier: 4.105A pdb=" N CYS 5 116 " --> pdb=" O ILE 5 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL 5 117 " --> pdb=" O ARG 5 113 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE 5 118 " --> pdb=" O ASN 5 114 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU 5 119 " --> pdb=" O VAL 5 115 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA 5 120 " --> pdb=" O CYS 5 116 " (cutoff:3.500A) Proline residue: 5 121 - end of helix removed outlier: 4.051A pdb=" N TYR 5 132 " --> pdb=" O THR 5 128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS 5 133 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU 5 137 " --> pdb=" O HIS 5 133 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU 5 138 " --> pdb=" O LEU 5 134 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS 5 139 " --> pdb=" O THR 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 140 through 154 removed outlier: 4.323A pdb=" N LEU 5 146 " --> pdb=" O GLY 5 142 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA 5 149 " --> pdb=" O LEU 5 145 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET 5 150 " --> pdb=" O LEU 5 146 " (cutoff:3.500A) Processing helix chain '5' and resid 155 through 162 removed outlier: 3.594A pdb=" N SER 5 161 " --> pdb=" O TYR 5 157 " (cutoff:3.500A) Processing helix chain '5' and resid 167 through 190 removed outlier: 4.604A pdb=" N ILE 5 171 " --> pdb=" O ASP 5 167 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ALA 5 172 " --> pdb=" O ASN 5 168 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE 5 173 " --> pdb=" O GLU 5 169 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N PHE 5 174 " --> pdb=" O GLY 5 170 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS 5 185 " --> pdb=" O TYR 5 181 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA 5 186 " --> pdb=" O MET 5 182 " (cutoff:3.500A) Processing helix chain '5' and resid 191 through 209 removed outlier: 4.082A pdb=" N TYR 5 204 " --> pdb=" O LEU 5 200 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET 5 205 " --> pdb=" O ALA 5 201 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER 5 208 " --> pdb=" O TYR 5 204 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP 5 209 " --> pdb=" O MET 5 205 " (cutoff:3.500A) Processing helix chain '5' and resid 210 through 230 removed outlier: 5.132A pdb=" N PHE 5 214 " --> pdb=" O GLY 5 210 " (cutoff:3.500A) Proline residue: 5 220 - end of helix removed outlier: 3.629A pdb=" N LEU 5 228 " --> pdb=" O LEU 5 224 " (cutoff:3.500A) Processing helix chain '5' and resid 233 through 255 removed outlier: 3.719A pdb=" N TYR 5 237 " --> pdb=" O SER 5 233 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA 5 239 " --> pdb=" O ARG 5 235 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR 5 242 " --> pdb=" O VAL 5 238 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL 5 243 " --> pdb=" O ALA 5 239 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE 5 249 " --> pdb=" O CYS 5 245 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE 5 254 " --> pdb=" O LEU 5 250 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER 5 255 " --> pdb=" O SER 5 251 " (cutoff:3.500A) Processing helix chain '5' and resid 259 through 264 removed outlier: 3.514A pdb=" N LEU 5 263 " --> pdb=" O PHE 5 259 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER 5 264 " --> pdb=" O GLN 5 260 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 259 through 264' Processing helix chain '5' and resid 265 through 291 removed outlier: 3.700A pdb=" N ALA 5 269 " --> pdb=" O SER 5 265 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG 5 287 " --> pdb=" O VAL 5 283 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER 5 288 " --> pdb=" O ASP 5 284 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS 5 289 " --> pdb=" O TYR 5 285 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU 5 290 " --> pdb=" O LEU 5 286 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASN 5 291 " --> pdb=" O ARG 5 287 " (cutoff:3.500A) Processing helix chain '5' and resid 293 through 318 removed outlier: 4.142A pdb=" N VAL 5 297 " --> pdb=" O GLN 5 293 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET 5 318 " --> pdb=" O GLY 5 314 " (cutoff:3.500A) Processing helix chain '5' and resid 356 through 365 removed outlier: 4.011A pdb=" N LEU 5 364 " --> pdb=" O TYR 5 360 " (cutoff:3.500A) Processing helix chain '5' and resid 366 through 382 removed outlier: 3.904A pdb=" N PHE 5 371 " --> pdb=" O LEU 5 367 " (cutoff:3.500A) Proline residue: 5 372 - end of helix removed outlier: 3.638A pdb=" N LEU 5 375 " --> pdb=" O PHE 5 371 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU 5 382 " --> pdb=" O CYS 5 378 " (cutoff:3.500A) Processing helix chain '5' and resid 383 through 403 removed outlier: 3.903A pdb=" N ILE 5 387 " --> pdb=" O SER 5 383 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE 5 388 " --> pdb=" O ASP 5 384 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE 5 389 " --> pdb=" O ALA 5 385 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER 5 396 " --> pdb=" O TYR 5 392 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET 5 397 " --> pdb=" O GLY 5 393 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL 5 402 " --> pdb=" O TYR 5 398 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET 5 403 " --> pdb=" O PHE 5 399 " (cutoff:3.500A) Processing helix chain '5' and resid 404 through 434 removed outlier: 4.628A pdb=" N LEU 5 408 " --> pdb=" O VAL 5 404 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL 5 409 " --> pdb=" O ARG 5 405 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU 5 410 " --> pdb=" O LEU 5 406 " (cutoff:3.500A) Proline residue: 5 412 - end of helix removed outlier: 4.275A pdb=" N CYS 5 415 " --> pdb=" O ALA 5 411 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER 5 423 " --> pdb=" O GLY 5 419 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN 5 432 " --> pdb=" O THR 5 428 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU 5 433 " --> pdb=" O TYR 5 429 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ASP 5 434 " --> pdb=" O MET 5 430 " (cutoff:3.500A) Processing helix chain '5' and resid 455 through 482 removed outlier: 5.034A pdb=" N LEU 5 462 " --> pdb=" O SER 5 458 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET 5 464 " --> pdb=" O MET 5 460 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA 5 465 " --> pdb=" O ILE 5 461 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE 5 466 " --> pdb=" O LEU 5 462 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR 5 470 " --> pdb=" O PHE 5 466 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR 5 471 " --> pdb=" O PHE 5 467 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR 5 472 " --> pdb=" O LEU 5 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP 5 477 " --> pdb=" O PHE 5 473 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR 5 479 " --> pdb=" O SER 5 475 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER 5 480 " --> pdb=" O THR 5 476 " (cutoff:3.500A) Processing helix chain '5' and resid 503 through 515 Processing helix chain '5' and resid 525 through 536 removed outlier: 4.089A pdb=" N GLY 5 529 " --> pdb=" O TRP 5 525 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR 5 530 " --> pdb=" O TRP 5 526 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN 5 531 " --> pdb=" O ASP 5 527 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE 5 532 " --> pdb=" O TYR 5 528 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR 5 533 " --> pdb=" O GLY 5 529 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET 5 535 " --> pdb=" O GLN 5 531 " (cutoff:3.500A) Processing helix chain '5' and resid 548 through 560 removed outlier: 4.089A pdb=" N ILE 5 552 " --> pdb=" O ASN 5 548 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL 5 555 " --> pdb=" O HIS 5 551 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY 5 556 " --> pdb=" O ILE 5 552 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN 5 557 " --> pdb=" O SER 5 553 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA 5 560 " --> pdb=" O GLY 5 556 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 574 Processing helix chain '5' and resid 591 through 596 removed outlier: 3.849A pdb=" N LYS 5 595 " --> pdb=" O ASP 5 591 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE 5 596 " --> pdb=" O ASP 5 592 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 591 through 596' Processing helix chain '5' and resid 597 through 602 Processing helix chain '5' and resid 608 through 613 removed outlier: 6.331A pdb=" N ILE 5 612 " --> pdb=" O THR 5 608 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS 5 613 " --> pdb=" O GLY 5 609 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 608 through 613' Processing helix chain '5' and resid 631 through 638 removed outlier: 5.186A pdb=" N LEU 5 638 " --> pdb=" O LEU 5 634 " (cutoff:3.500A) Processing helix chain '5' and resid 639 through 644 removed outlier: 3.526A pdb=" N CYS 5 643 " --> pdb=" O MET 5 639 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR 5 644 " --> pdb=" O TYR 5 640 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 639 through 644' Processing helix chain '5' and resid 646 through 651 removed outlier: 3.602A pdb=" N VAL 5 650 " --> pdb=" O ARG 5 646 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR 5 651 " --> pdb=" O PHE 5 647 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 646 through 651' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.889A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.523A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 removed outlier: 3.593A pdb=" N ARG A 72 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 146 through 150 removed outlier: 4.362A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 40 through 44 removed outlier: 4.792A pdb=" N GLY B 188 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN B 184 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 45 through 50 removed outlier: 4.051A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 53 through 59 Processing sheet with id= 8, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.537A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 88 through 93 removed outlier: 3.710A pdb=" N VAL B 159 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.959A pdb=" N GLU B 215 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 7 through 10 removed outlier: 4.977A pdb=" N LYS C 20 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 226 through 232 removed outlier: 3.616A pdb=" N THR C 228 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N PHE C 249 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 60 through 66 removed outlier: 3.509A pdb=" N TYR D 145 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 143 through 149 removed outlier: 4.082A pdb=" N THR E 144 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS E 156 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 158 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY E 173 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE E 160 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 171 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS E 162 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU E 169 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU E 164 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 141 through 146 removed outlier: 7.105A pdb=" N TYR F 141 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N PHE F 120 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 161 through 164 Processing sheet with id= 17, first strand: chain 'G' and resid 180 through 185 removed outlier: 3.847A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR G 200 " --> pdb=" O ALA G 158 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 5 through 12 removed outlier: 5.665A pdb=" N LYS H 53 " --> pdb=" O ILE H 12 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 20, first strand: chain 'H' and resid 102 through 106 removed outlier: 6.468A pdb=" N LEU H 111 " --> pdb=" O GLN H 106 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER H 110 " --> pdb=" O MET H 128 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG H 124 " --> pdb=" O ILE H 114 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 132 through 136 removed outlier: 5.901A pdb=" N ASP H 142 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS H 91 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 88 through 91 Processing sheet with id= 23, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.075A pdb=" N PHE I 34 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE I 135 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET I 136 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR I 140 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU I 48 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N CYS I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 95 through 98 removed outlier: 3.562A pdb=" N GLY I 124 " --> pdb=" O ILE I 97 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 189 through 192 removed outlier: 4.859A pdb=" N ARG I 189 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 48 through 52 removed outlier: 3.662A pdb=" N ASP J 129 " --> pdb=" O ASN J 23 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS J 25 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLY J 127 " --> pdb=" O CYS J 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE J 105 " --> pdb=" O VAL J 132 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 92 through 95 removed outlier: 6.443A pdb=" N LEU J 94 " --> pdb=" O ILE J 173 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 11 through 15 removed outlier: 4.330A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS M 23 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.635A pdb=" N ARG M 35 " --> pdb=" O ILE M 31 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.592A pdb=" N ALA N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY N 58 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 117 through 121 removed outlier: 6.516A pdb=" N PHE N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 33, first strand: chain 'P' and resid 16 through 20 Processing sheet with id= 34, first strand: chain 'P' and resid 57 through 60 removed outlier: 4.174A pdb=" N PHE P 60 " --> pdb=" O GLN P 80 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLN P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'P' and resid 124 through 131 removed outlier: 3.918A pdb=" N SER P 141 " --> pdb=" O MET P 125 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 78 through 82 Processing sheet with id= 37, first strand: chain 'S' and resid 27 through 33 removed outlier: 3.627A pdb=" N VAL S 12 " --> pdb=" O MET S 30 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 91 through 99 removed outlier: 3.981A pdb=" N MET S 93 " --> pdb=" O LEU S 82 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS S 128 " --> pdb=" O TRP S 81 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 9 through 13 removed outlier: 4.743A pdb=" N GLU S 9 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 38 through 42 removed outlier: 4.227A pdb=" N ASP T 38 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 61 through 65 removed outlier: 3.559A pdb=" N THR U 71 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE U 70 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU U 108 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR U 110 " --> pdb=" O THR U 22 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 76 through 80 removed outlier: 6.737A pdb=" N MET V 62 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE V 26 " --> pdb=" O LEU V 37 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA V 24 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASN V 101 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN V 27 " --> pdb=" O ASN V 101 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP V 100 " --> pdb=" O ARG V 85 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG V 85 " --> pdb=" O ASP V 100 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 87 through 90 removed outlier: 3.995A pdb=" N VAL V 94 " --> pdb=" O ARG V 90 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 18 through 22 Processing sheet with id= 45, first strand: chain 'X' and resid 95 through 100 removed outlier: 3.891A pdb=" N LYS X 134 " --> pdb=" O VAL X 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR X 137 " --> pdb=" O ASN X 125 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Y' and resid 53 through 56 removed outlier: 4.986A pdb=" N ASP Y 53 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Y' and resid 71 through 75 Processing sheet with id= 48, first strand: chain 'Y' and resid 85 through 89 removed outlier: 6.315A pdb=" N VAL Y 85 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Z' and resid 10 through 13 removed outlier: 3.995A pdb=" N ARG Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Z' and resid 27 through 30 removed outlier: 5.757A pdb=" N HIS Z 40 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'a' and resid 98 through 101 Processing sheet with id= 52, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.622A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY c 70 " --> pdb=" O LYS c 44 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 20 through 27 removed outlier: 4.208A pdb=" N VAL d 21 " --> pdb=" O ARG d 90 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG d 85 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR d 103 " --> pdb=" O LYS d 91 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP d 61 " --> pdb=" O LEU d 102 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL d 106 " --> pdb=" O ARG d 63 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 74 through 80 Processing sheet with id= 55, first strand: chain 'f' and resid 9 through 12 removed outlier: 6.744A pdb=" N LEU f 27 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS f 45 " --> pdb=" O VAL f 74 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ARG f 46 " --> pdb=" O MET f 104 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 6 through 11 removed outlier: 4.580A pdb=" N HIS f 99 " --> pdb=" O PHE f 11 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 19 through 24 removed outlier: 5.308A pdb=" N LYS g 19 " --> pdb=" O THR g 35 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.360A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL k 32 " --> pdb=" O ILE k 47 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER k 22 " --> pdb=" O ARG k 37 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS k 67 " --> pdb=" O VAL k 23 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE k 25 " --> pdb=" O LYS k 67 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS k 27 " --> pdb=" O LEU k 69 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 100 through 104 removed outlier: 4.337A pdb=" N ALA m 101 " --> pdb=" O CYS m 96 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS m 93 " --> pdb=" O LYS m 124 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN m 120 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'o' and resid 7 through 10 removed outlier: 3.580A pdb=" N THR o 24 " --> pdb=" O ARG o 69 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.751A pdb=" N LYS p 46 " --> pdb=" O GLY p 58 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY p 58 " --> pdb=" O LYS p 46 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'r' and resid 48 through 53 removed outlier: 4.753A pdb=" N THR r 48 " --> pdb=" O LYS r 65 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 's' and resid 51 through 55 removed outlier: 8.127A pdb=" N ASN s 85 " --> pdb=" O ALA s 32 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS s 26 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN s 191 " --> pdb=" O ILE s 29 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR s 199 " --> pdb=" O VAL s 192 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 's' and resid 144 through 147 removed outlier: 7.433A pdb=" N THR s 144 " --> pdb=" O LEU s 155 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 't' and resid 11 through 20 removed outlier: 5.628A pdb=" N THR t 59 " --> pdb=" O THR t 18 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY t 20 " --> pdb=" O ARG t 57 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG t 57 " --> pdb=" O GLY t 20 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU t 62 " --> pdb=" O VAL t 73 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE t 64 " --> pdb=" O ILE t 71 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'x' and resid 263 through 266 Processing sheet with id= 67, first strand: chain '5' and resid 521 through 524 removed outlier: 3.935A pdb=" N TYR 5 577 " --> pdb=" O LYS 5 521 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET 5 523 " --> pdb=" O TYR 5 577 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER 5 576 " --> pdb=" O VAL 5 694 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL 5 694 " --> pdb=" O SER 5 576 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL 5 580 " --> pdb=" O ARG 5 690 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG 5 690 " --> pdb=" O VAL 5 580 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU 5 688 " --> pdb=" O PHE 5 582 " (cutoff:3.500A) 2759 hydrogen bonds defined for protein. 8181 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3230 hydrogen bonds 5630 hydrogen bond angles 0 basepair planarities 1230 basepair parallelities 1953 stacking parallelities Total time for adding SS restraints: 318.32 Time building geometry restraints manager: 64.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.32: 18826 1.32 - 1.73: 145755 1.73 - 2.14: 521 2.14 - 2.56: 1 2.56 - 2.97: 6 Bond restraints: 165109 Sorted by residual: bond pdb=" C PHE 5 502 " pdb=" N ASP 5 503 " ideal model delta sigma weight residual 1.330 2.784 -1.454 1.28e-02 6.10e+03 1.29e+04 bond pdb=" O3' G u1840 " pdb=" P G u1842 " ideal model delta sigma weight residual 1.607 2.911 -1.304 1.50e-02 4.44e+03 7.56e+03 bond pdb=" O3' C u4939 " pdb=" P G u4941 " ideal model delta sigma weight residual 1.607 2.805 -1.198 1.50e-02 4.44e+03 6.38e+03 bond pdb=" C GLN r 121 " pdb=" N LYS r 122 " ideal model delta sigma weight residual 1.331 2.965 -1.634 2.07e-02 2.33e+03 6.23e+03 bond pdb=" O3' C u4942 " pdb=" P C u4944 " ideal model delta sigma weight residual 1.607 2.733 -1.126 1.50e-02 4.44e+03 5.63e+03 ... (remaining 165104 not shown) Histogram of bond angle deviations from ideal: 60.45 - 81.84: 6 81.84 - 103.23: 11904 103.23 - 124.61: 213063 124.61 - 146.00: 17549 146.00 - 167.39: 2 Bond angle restraints: 242524 Sorted by residual: angle pdb=" O SER 5 590 " pdb=" C SER 5 590 " pdb=" N ASP 5 591 " ideal model delta sigma weight residual 122.59 60.45 62.14 1.33e+00 5.65e-01 2.18e+03 angle pdb=" C3' G u1840 " pdb=" O3' G u1840 " pdb=" P G u1842 " ideal model delta sigma weight residual 120.20 81.73 38.47 1.50e+00 4.44e-01 6.58e+02 angle pdb=" O3' G u1840 " pdb=" P G u1842 " pdb=" O5' G u1842 " ideal model delta sigma weight residual 104.00 67.04 36.96 1.50e+00 4.44e-01 6.07e+02 angle pdb=" C ASN 5 545 " pdb=" N THR 5 546 " pdb=" CA THR 5 546 " ideal model delta sigma weight residual 121.54 79.46 42.08 1.91e+00 2.74e-01 4.85e+02 angle pdb=" O3' C u4939 " pdb=" P G u4941 " pdb=" O5' G u4941 " ideal model delta sigma weight residual 104.00 72.26 31.74 1.50e+00 4.44e-01 4.48e+02 ... (remaining 242519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 92750 35.92 - 71.85: 11899 71.85 - 107.77: 1469 107.77 - 143.69: 85 143.69 - 179.61: 128 Dihedral angle restraints: 106331 sinusoidal: 81505 harmonic: 24826 Sorted by residual: dihedral pdb=" CA LEU B 17 " pdb=" C LEU B 17 " pdb=" N PRO B 18 " pdb=" CA PRO B 18 " ideal model delta harmonic sigma weight residual 180.00 100.11 79.89 0 5.00e+00 4.00e-02 2.55e+02 dihedral pdb=" CA PHE 5 502 " pdb=" C PHE 5 502 " pdb=" N ASP 5 503 " pdb=" CA ASP 5 503 " ideal model delta harmonic sigma weight residual -180.00 -122.08 -57.92 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA LEU r 106 " pdb=" C LEU r 106 " pdb=" N ARG r 107 " pdb=" CA ARG r 107 " ideal model delta harmonic sigma weight residual -180.00 -122.67 -57.33 0 5.00e+00 4.00e-02 1.31e+02 ... (remaining 106328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 26419 0.164 - 0.328: 3673 0.328 - 0.493: 110 0.493 - 0.657: 40 0.657 - 0.821: 9 Chirality restraints: 30251 Sorted by residual: chirality pdb=" C3' G u2046 " pdb=" C4' G u2046 " pdb=" O3' G u2046 " pdb=" C2' G u2046 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" C3' C u2068 " pdb=" C4' C u2068 " pdb=" O3' C u2068 " pdb=" C2' C u2068 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" C3' G u 48 " pdb=" C4' G u 48 " pdb=" O3' G u 48 " pdb=" C2' G u 48 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.77 2.00e-01 2.50e+01 1.49e+01 ... (remaining 30248 not shown) Planarity restraints: 15719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER 5 590 " -0.173 2.00e-02 2.50e+03 2.52e-01 6.33e+02 pdb=" C SER 5 590 " 0.385 2.00e-02 2.50e+03 pdb=" O SER 5 590 " -0.269 2.00e-02 2.50e+03 pdb=" N ASP 5 591 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE 5 532 " 0.060 2.00e-02 2.50e+03 1.07e-01 1.14e+02 pdb=" C ILE 5 532 " -0.185 2.00e-02 2.50e+03 pdb=" O ILE 5 532 " 0.068 2.00e-02 2.50e+03 pdb=" N THR 5 533 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G u2793 " 0.078 2.00e-02 2.50e+03 5.29e-02 8.41e+01 pdb=" N9 G u2793 " -0.037 2.00e-02 2.50e+03 pdb=" C8 G u2793 " -0.013 2.00e-02 2.50e+03 pdb=" N7 G u2793 " -0.016 2.00e-02 2.50e+03 pdb=" C5 G u2793 " -0.046 2.00e-02 2.50e+03 pdb=" C6 G u2793 " -0.024 2.00e-02 2.50e+03 pdb=" O6 G u2793 " 0.121 2.00e-02 2.50e+03 pdb=" N1 G u2793 " -0.086 2.00e-02 2.50e+03 pdb=" C2 G u2793 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G u2793 " 0.031 2.00e-02 2.50e+03 pdb=" N3 G u2793 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G u2793 " -0.007 2.00e-02 2.50e+03 ... (remaining 15716 not shown) Histogram of nonbonded interaction distances: 0.28 - 1.21: 18 1.21 - 2.13: 238 2.13 - 3.05: 92993 3.05 - 3.98: 492498 3.98 - 4.90: 814208 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1399955 Sorted by model distance: nonbonded pdb=" CB GLU X 84 " pdb=" CG HIS x 404 " model vdw 0.284 3.660 nonbonded pdb=" O3' U u2432 " pdb=" NZ LYS x 268 " model vdw 0.543 2.520 nonbonded pdb=" CA GLU X 84 " pdb=" CD2 HIS x 404 " model vdw 0.556 3.690 nonbonded pdb=" NH1 ARG l 21 " pdb=" NH1 ARG x 273 " model vdw 0.630 3.200 nonbonded pdb=" CA VAL z 73 " pdb=" CE MET z 76 " model vdw 0.639 3.890 ... (remaining 1399950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = (chain '7' and resid 416 through 439) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.910 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: 0.150 Extract box with map and model: 30.380 Check model and map are aligned: 1.650 Set scattering table: 1.020 Process input model: 641.600 Find NCS groups from input model: 3.120 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:1.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 690.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 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 1.634 165109 Z= 0.723 Angle : 1.384 62.139 242524 Z= 0.905 Chirality : 0.103 0.821 30251 Planarity : 0.009 0.252 15718 Dihedral : 25.552 179.613 90307 Min Nonbonded Distance : 0.284 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 2.37 % Allowed : 9.74 % Favored : 87.88 % Rotamer: Outliers : 11.77 % Allowed : 12.51 % Favored : 75.73 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.36 % 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: -4.07 (0.08), residues: 8221 helix: -2.30 (0.07), residues: 3180 sheet: -3.20 (0.13), residues: 930 loop : -2.90 (0.08), residues: 4111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP 5 71 HIS 0.023 0.003 HIS 5 267 PHE 0.047 0.004 PHE 3 101 TYR 0.049 0.004 TYR E 53 ARG 0.027 0.001 ARG x 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3298 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 814 poor density : 2484 time to evaluate : 7.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.8559 (mtm110) cc_final: 0.7991 (mtm-85) REVERT: A 41 ILE cc_start: 0.6527 (tp) cc_final: 0.5926 (tp) REVERT: A 89 TYR cc_start: 0.5469 (m-80) cc_final: 0.5205 (m-80) REVERT: A 198 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7404 (ttt90) REVERT: A 217 GLN cc_start: 0.8224 (mt0) cc_final: 0.7679 (pt0) REVERT: A 238 ILE cc_start: 0.7205 (mm) cc_final: 0.6921 (mm) REVERT: B 21 ARG cc_start: 0.4696 (OUTLIER) cc_final: 0.4415 (mtp85) REVERT: B 53 MET cc_start: 0.5129 (mmt) cc_final: 0.4605 (mmt) REVERT: B 103 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6383 (mmtt) REVERT: B 118 PHE cc_start: 0.4757 (m-80) cc_final: 0.4533 (m-80) REVERT: B 146 LEU cc_start: 0.1212 (OUTLIER) cc_final: 0.0990 (tt) REVERT: C 65 GLU cc_start: 0.8947 (tp30) cc_final: 0.8499 (tp30) REVERT: C 100 ARG cc_start: 0.4816 (tmm160) cc_final: 0.4269 (tmm160) REVERT: C 101 MET cc_start: 0.5012 (OUTLIER) cc_final: 0.4175 (ptm) REVERT: C 195 LYS cc_start: 0.4934 (OUTLIER) cc_final: 0.4426 (mtpt) REVERT: C 249 PHE cc_start: 0.5212 (t80) cc_final: 0.5006 (t80) REVERT: D 34 LYS cc_start: 0.7534 (tttt) cc_final: 0.7228 (pttm) REVERT: D 146 LEU cc_start: 0.4313 (tm) cc_final: 0.3691 (tm) REVERT: D 208 MET cc_start: 0.5668 (OUTLIER) cc_final: 0.4898 (ttm) REVERT: D 239 MET cc_start: 0.4246 (OUTLIER) cc_final: 0.3258 (tmm) REVERT: D 275 GLN cc_start: 0.5855 (mt0) cc_final: 0.5002 (mm-40) REVERT: D 284 LYS cc_start: 0.5336 (OUTLIER) cc_final: 0.4491 (mmtt) REVERT: E 170 LEU cc_start: 0.3538 (tp) cc_final: 0.3122 (tp) REVERT: E 204 ILE cc_start: 0.7612 (tp) cc_final: 0.7276 (tp) REVERT: F 41 GLN cc_start: 0.5140 (OUTLIER) cc_final: 0.4643 (mt0) REVERT: G 109 GLU cc_start: 0.6914 (tp30) cc_final: 0.6276 (tm-30) REVERT: G 149 ASN cc_start: 0.6472 (t0) cc_final: 0.6253 (m-40) REVERT: G 165 GLU cc_start: 0.6132 (mp0) cc_final: 0.5540 (tp30) REVERT: G 173 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6113 (tp) REVERT: H 15 ASN cc_start: 0.5850 (t0) cc_final: 0.5195 (m-40) REVERT: H 102 ASN cc_start: 0.8095 (t0) cc_final: 0.7799 (m110) REVERT: H 120 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6760 (mm-30) REVERT: H 125 ARG cc_start: 0.6231 (OUTLIER) cc_final: 0.5955 (ptm160) REVERT: I 5 PRO cc_start: 0.7093 (Cg_exo) cc_final: 0.6854 (Cg_endo) REVERT: I 116 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.5697 (ptt180) REVERT: I 159 PHE cc_start: 0.6944 (m-80) cc_final: 0.6604 (m-10) REVERT: I 174 THR cc_start: 0.6427 (p) cc_final: 0.5492 (p) REVERT: I 206 LEU cc_start: 0.6798 (tp) cc_final: 0.6570 (mt) REVERT: I 207 ASP cc_start: 0.7199 (m-30) cc_final: 0.6029 (t0) REVERT: I 209 TRP cc_start: 0.5200 (t60) cc_final: 0.4976 (t60) REVERT: J 28 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7220 (mt-10) REVERT: L 8 MET cc_start: 0.6586 (mtt) cc_final: 0.5869 (mtp) REVERT: L 90 VAL cc_start: 0.7418 (t) cc_final: 0.7150 (p) REVERT: L 99 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6846 (p0) REVERT: L 143 GLU cc_start: 0.2802 (OUTLIER) cc_final: 0.1869 (tt0) REVERT: L 169 ILE cc_start: 0.3779 (mt) cc_final: 0.2798 (mt) REVERT: L 184 MET cc_start: 0.7735 (mmm) cc_final: 0.7373 (tpt) REVERT: L 190 ARG cc_start: 0.4549 (OUTLIER) cc_final: 0.3945 (tpm170) REVERT: M 4 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.3709 (mmt180) REVERT: M 53 LYS cc_start: 0.5230 (OUTLIER) cc_final: 0.4828 (tptt) REVERT: M 118 MET cc_start: 0.6894 (tpt) cc_final: 0.6484 (tpt) REVERT: N 26 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.6003 (mtp180) REVERT: N 77 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.7061 (mmtm) REVERT: N 161 MET cc_start: 0.7116 (mmm) cc_final: 0.6913 (mmp) REVERT: O 5 GLN cc_start: 0.4676 (OUTLIER) cc_final: 0.2368 (tp40) REVERT: O 9 LEU cc_start: 0.5441 (mt) cc_final: 0.5108 (mt) REVERT: O 31 ARG cc_start: 0.4154 (OUTLIER) cc_final: 0.3781 (tpt-90) REVERT: O 52 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6379 (mt) REVERT: O 109 PRO cc_start: 0.6759 (Cg_endo) cc_final: 0.6471 (Cg_exo) REVERT: O 118 MET cc_start: 0.4663 (mmp) cc_final: 0.3777 (mmm) REVERT: O 171 LYS cc_start: 0.2501 (tttt) cc_final: 0.2211 (tptt) REVERT: P 41 ILE cc_start: 0.7907 (tt) cc_final: 0.7459 (mm) REVERT: P 43 LYS cc_start: 0.6740 (tttm) cc_final: 0.6308 (tptm) REVERT: P 91 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7493 (pp) REVERT: P 94 MET cc_start: 0.6180 (ttm) cc_final: 0.5828 (mmm) REVERT: P 100 SER cc_start: 0.7880 (OUTLIER) cc_final: 0.7570 (t) REVERT: P 101 ASN cc_start: 0.5124 (m-40) cc_final: 0.4355 (t0) REVERT: P 110 ASP cc_start: 0.8354 (p0) cc_final: 0.7876 (t0) REVERT: P 114 ILE cc_start: 0.6941 (tt) cc_final: 0.6703 (tt) REVERT: Q 9 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.5921 (mmtt) REVERT: Q 54 SER cc_start: 0.7442 (OUTLIER) cc_final: 0.7024 (t) REVERT: Q 87 THR cc_start: 0.7435 (p) cc_final: 0.6600 (t) REVERT: R 10 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6630 (mt) REVERT: R 25 ASP cc_start: 0.8613 (t70) cc_final: 0.8362 (t0) REVERT: R 66 ASN cc_start: 0.8478 (m-40) cc_final: 0.8232 (m110) REVERT: S 9 GLU cc_start: 0.4764 (OUTLIER) cc_final: 0.4557 (tp30) REVERT: U 97 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.5504 (mmm160) REVERT: U 112 LEU cc_start: 0.8199 (mt) cc_final: 0.7960 (mm) REVERT: V 31 ASN cc_start: 0.0714 (OUTLIER) cc_final: 0.0479 (p0) REVERT: V 99 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5471 (tm-30) REVERT: W 43 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7789 (tmmt) REVERT: X 109 ILE cc_start: 0.6990 (mt) cc_final: 0.6704 (mt) REVERT: X 131 ASP cc_start: 0.8455 (m-30) cc_final: 0.8054 (m-30) REVERT: Y 10 ASP cc_start: 0.7706 (t70) cc_final: 0.7482 (m-30) REVERT: Y 14 ASN cc_start: 0.8588 (m-40) cc_final: 0.7685 (t0) REVERT: Y 59 ARG cc_start: 0.4834 (OUTLIER) cc_final: 0.4351 (ttm110) REVERT: Y 62 TYR cc_start: 0.5833 (m-80) cc_final: 0.5296 (m-80) REVERT: Z 28 ASN cc_start: 0.6784 (p0) cc_final: 0.6439 (t0) REVERT: a 12 ARG cc_start: 0.5486 (OUTLIER) cc_final: 0.3717 (mmt180) REVERT: a 58 MET cc_start: 0.2468 (mtm) cc_final: 0.1829 (tpt) REVERT: a 146 LEU cc_start: 0.6522 (mt) cc_final: 0.6316 (mp) REVERT: b 44 ARG cc_start: 0.6996 (mtt-85) cc_final: 0.6379 (ttt180) REVERT: b 57 MET cc_start: 0.3415 (ttm) cc_final: 0.2251 (tpt) REVERT: c 40 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.6096 (mm110) REVERT: d 19 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6048 (pt0) REVERT: d 20 VAL cc_start: 0.7106 (m) cc_final: 0.6815 (t) REVERT: d 25 TYR cc_start: 0.6746 (m-80) cc_final: 0.6414 (m-80) REVERT: d 67 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8335 (mmp80) REVERT: d 78 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6358 (mtm-85) REVERT: d 94 GLU cc_start: 0.4786 (OUTLIER) cc_final: 0.3627 (mp0) REVERT: e 9 LYS cc_start: 0.5627 (OUTLIER) cc_final: 0.5369 (mttt) REVERT: e 21 ILE cc_start: 0.1440 (OUTLIER) cc_final: 0.1176 (tt) REVERT: e 38 PRO cc_start: 0.5770 (Cg_exo) cc_final: 0.4542 (Cg_exo) REVERT: e 93 LYS cc_start: 0.7653 (mptm) cc_final: 0.7226 (mtpt) REVERT: f 52 LYS cc_start: 0.5691 (OUTLIER) cc_final: 0.4788 (mtmm) REVERT: f 100 ARG cc_start: 0.3250 (OUTLIER) cc_final: 0.1117 (ptt90) REVERT: g 11 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6640 (mp) REVERT: g 18 ASN cc_start: 0.7634 (t0) cc_final: 0.7201 (t0) REVERT: g 32 TYR cc_start: 0.8597 (m-10) cc_final: 0.8396 (m-80) REVERT: g 64 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6480 (mt) REVERT: h 54 ILE cc_start: 0.9141 (mt) cc_final: 0.8826 (mt) REVERT: h 58 LEU cc_start: 0.8811 (mt) cc_final: 0.8510 (mt) REVERT: i 58 MET cc_start: 0.4754 (mmm) cc_final: 0.3955 (ppp) REVERT: i 62 LYS cc_start: 0.6869 (mttt) cc_final: 0.6516 (tttt) REVERT: j 79 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5812 (ptp90) REVERT: k 39 SER cc_start: 0.6648 (OUTLIER) cc_final: 0.6050 (m) REVERT: k 47 ILE cc_start: 0.6236 (mm) cc_final: 0.5895 (mm) REVERT: l 10 LYS cc_start: 0.8890 (tttt) cc_final: 0.8663 (ttmm) REVERT: l 36 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7456 (mtt90) REVERT: l 46 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8222 (ptp90) REVERT: l 47 THR cc_start: 0.9116 (m) cc_final: 0.8770 (p) REVERT: n 2 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.4833 (mtm180) REVERT: n 12 ARG cc_start: 0.5014 (mtt180) cc_final: 0.4771 (mtt-85) REVERT: n 13 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7581 (tt) REVERT: n 14 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8100 (mmtt) REVERT: o 6 LYS cc_start: 0.7614 (mtmm) cc_final: 0.7242 (mtpp) REVERT: r 40 TYR cc_start: 0.7338 (m-10) cc_final: 0.6956 (m-10) REVERT: r 63 VAL cc_start: 0.5856 (t) cc_final: 0.4470 (p) REVERT: s 15 LEU cc_start: 0.8336 (mt) cc_final: 0.8093 (tp) REVERT: s 76 GLU cc_start: 0.1276 (mt-10) cc_final: 0.0944 (pp20) REVERT: s 174 LEU cc_start: 0.2533 (OUTLIER) cc_final: 0.1536 (pp) REVERT: t 1 MET cc_start: -0.5024 (OUTLIER) cc_final: -0.5488 (mtp) REVERT: t 123 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.5237 (pmt170) REVERT: t 124 GLU cc_start: 0.2186 (OUTLIER) cc_final: 0.1598 (pt0) REVERT: x 64 TRP cc_start: 0.8778 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: x 116 GLN cc_start: 0.7323 (tp-100) cc_final: 0.6937 (tp40) REVERT: x 163 LEU cc_start: 0.9326 (mt) cc_final: 0.8913 (mt) REVERT: x 171 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8354 (ptmm) REVERT: x 364 TYR cc_start: 0.8559 (t80) cc_final: 0.8153 (t80) REVERT: x 392 LYS cc_start: 0.9162 (mttp) cc_final: 0.8925 (mmtp) REVERT: y 38 MET cc_start: 0.7136 (ttp) cc_final: 0.6654 (mmt) REVERT: 1 451 PHE cc_start: 0.8146 (t80) cc_final: 0.7860 (t80) REVERT: 1 455 ILE cc_start: 0.9200 (mt) cc_final: 0.8936 (mt) REVERT: 1 458 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6848 (ttp-170) REVERT: 3 31 MET cc_start: 0.8702 (mmm) cc_final: 0.8449 (mmp) REVERT: 3 42 PHE cc_start: 0.9011 (p90) cc_final: 0.8581 (p90) REVERT: 3 85 MET cc_start: 0.8259 (tmm) cc_final: 0.7924 (tmm) REVERT: 3 94 PHE cc_start: 0.8915 (m-10) cc_final: 0.8570 (m-80) REVERT: 3 95 THR cc_start: 0.8585 (p) cc_final: 0.8358 (p) REVERT: 4 12 ASN cc_start: 0.8822 (m-40) cc_final: 0.8537 (m110) REVERT: 5 1 MET cc_start: -0.0780 (ttp) cc_final: -0.2054 (mtm) REVERT: 5 4 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3872 (tt) REVERT: 5 25 MET cc_start: 0.9145 (ptt) cc_final: 0.8620 (ppp) REVERT: 5 35 LEU cc_start: 0.9467 (mt) cc_final: 0.9206 (mt) REVERT: 5 78 TYR cc_start: 0.8641 (t80) cc_final: 0.8381 (t80) REVERT: 5 82 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5650 (ptp-170) REVERT: 5 114 ASN cc_start: 0.8763 (m110) cc_final: 0.7157 (m-40) REVERT: 5 118 PHE cc_start: 0.8322 (m-10) cc_final: 0.7320 (m-10) REVERT: 5 274 PHE cc_start: 0.6564 (t80) cc_final: 0.5908 (t80) REVERT: 5 278 GLN cc_start: 0.8454 (pt0) cc_final: 0.8075 (pt0) REVERT: 5 285 TYR cc_start: 0.2725 (OUTLIER) cc_final: 0.1019 (t80) REVERT: 5 361 TYR cc_start: 0.8520 (t80) cc_final: 0.7903 (t80) REVERT: 5 398 TYR cc_start: 0.8795 (t80) cc_final: 0.8558 (t80) REVERT: 5 406 LEU cc_start: 0.9473 (tp) cc_final: 0.9070 (tp) REVERT: 5 410 LEU cc_start: 0.9294 (mt) cc_final: 0.8987 (mt) REVERT: 5 414 MET cc_start: 0.8952 (mmt) cc_final: 0.8741 (mmt) REVERT: 5 429 TYR cc_start: 0.8115 (m-80) cc_final: 0.7893 (m-10) REVERT: 5 469 ILE cc_start: 0.9311 (pt) cc_final: 0.8867 (tp) REVERT: 5 483 TYR cc_start: 0.8109 (m-80) cc_final: 0.7692 (m-80) REVERT: 5 511 TRP cc_start: 0.6598 (t60) cc_final: 0.6208 (m100) REVERT: 5 597 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8193 (tp) REVERT: 5 693 LYS cc_start: 0.5618 (tttt) cc_final: 0.5378 (ttpt) outliers start: 814 outliers final: 133 residues processed: 2999 average time/residue: 1.6495 time to fit residues: 8169.1828 Evaluate side-chains 1666 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1474 time to evaluate : 7.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 1041 optimal weight: 20.0000 chunk 934 optimal weight: 9.9990 chunk 518 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 630 optimal weight: 8.9990 chunk 499 optimal weight: 3.9990 chunk 966 optimal weight: 9.9990 chunk 373 optimal weight: 9.9990 chunk 587 optimal weight: 3.9990 chunk 719 optimal weight: 20.0000 chunk 1119 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 HIS ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 212 ASN C 282 HIS C 310 HIS C 338 ASN C 343 GLN D 157 ASN D 225 GLN D 244 HIS ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN F 41 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN H 42 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN J 112 HIS L 19 GLN L 28 GLN L 104 ASN M 20 HIS ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 HIS ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 ASN S 122 HIS S 125 GLN T 70 HIS T 144 ASN W 50 ASN X 93 ASN Y 91 ASN Y 96 HIS ** a 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 44 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 72 HIS ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN e 43 ASN e 102 ASN h 107 GLN i 80 HIS l 38 ASN m 90 ASN ** m 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 HIS ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 ASN r 41 ASN ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 ASN s 72 ASN s 81 HIS s 191 GLN t 68 GLN t 115 GLN ** x 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 170 GLN ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 ASN x 393 GLN ** x 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 411 HIS 4 12 ASN 5 46 HIS ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 381 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.254 165109 Z= 0.369 Angle : 0.980 19.229 242524 Z= 0.491 Chirality : 0.050 0.409 30251 Planarity : 0.008 0.223 15718 Dihedral : 25.796 179.958 73507 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.34 % Favored : 91.81 % Rotamer: Outliers : 0.52 % Allowed : 6.64 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 2.08 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.08), residues: 8227 helix: -0.71 (0.08), residues: 3243 sheet: -2.47 (0.14), residues: 938 loop : -2.30 (0.09), residues: 4046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 196 HIS 0.037 0.003 HIS N 87 PHE 0.082 0.004 PHE 5 256 TYR 0.048 0.004 TYR Y 74 ARG 0.049 0.001 ARG x 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1786 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1750 time to evaluate : 7.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7798 (mmmt) REVERT: A 68 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6854 (ttt-90) REVERT: A 190 LYS cc_start: 0.8899 (ptmt) cc_final: 0.8355 (tptt) REVERT: A 198 ARG cc_start: 0.8417 (ttt180) cc_final: 0.7927 (ttt90) REVERT: A 217 GLN cc_start: 0.8494 (mt0) cc_final: 0.7825 (pt0) REVERT: B 32 PHE cc_start: 0.4233 (m-80) cc_final: 0.4026 (m-80) REVERT: B 69 LYS cc_start: 0.7803 (mmtm) cc_final: 0.7577 (mtmm) REVERT: B 118 PHE cc_start: 0.5306 (m-80) cc_final: 0.4849 (m-80) REVERT: B 168 MET cc_start: 0.3922 (tpt) cc_final: 0.3405 (tpt) REVERT: B 211 PHE cc_start: 0.4821 (m-10) cc_final: 0.4484 (m-10) REVERT: B 363 ILE cc_start: 0.6113 (mp) cc_final: 0.5633 (mp) REVERT: C 63 SER cc_start: 0.8455 (p) cc_final: 0.8155 (p) REVERT: C 65 GLU cc_start: 0.9074 (tp30) cc_final: 0.8626 (pm20) REVERT: C 95 MET cc_start: 0.8436 (pmm) cc_final: 0.8211 (pmm) REVERT: C 101 MET cc_start: 0.5130 (ptm) cc_final: 0.4433 (tpt) REVERT: C 189 MET cc_start: 0.6964 (ttm) cc_final: 0.6675 (ttt) REVERT: C 213 GLU cc_start: 0.6333 (pm20) cc_final: 0.5618 (mm-30) REVERT: D 109 LEU cc_start: 0.7771 (tp) cc_final: 0.7417 (tt) REVERT: D 113 PHE cc_start: 0.6080 (m-80) cc_final: 0.5876 (m-10) REVERT: D 135 ILE cc_start: 0.6956 (mm) cc_final: 0.5845 (mm) REVERT: D 207 TYR cc_start: 0.5767 (t80) cc_final: 0.5009 (t80) REVERT: D 275 GLN cc_start: 0.6474 (mt0) cc_final: 0.5878 (mm-40) REVERT: E 163 GLN cc_start: 0.6541 (tp40) cc_final: 0.5513 (tm-30) REVERT: E 250 ASP cc_start: 0.4038 (OUTLIER) cc_final: 0.3455 (p0) REVERT: F 76 MET cc_start: 0.8402 (tmm) cc_final: 0.8098 (tmm) REVERT: F 112 GLN cc_start: 0.6584 (mp10) cc_final: 0.5822 (pp30) REVERT: F 184 TYR cc_start: 0.5728 (m-80) cc_final: 0.5500 (m-80) REVERT: H 60 TRP cc_start: 0.4804 (m-90) cc_final: 0.4242 (m-90) REVERT: H 102 ASN cc_start: 0.8082 (t0) cc_final: 0.7765 (m-40) REVERT: H 116 ASN cc_start: 0.8194 (t0) cc_final: 0.7467 (t0) REVERT: H 120 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6840 (mm-30) REVERT: I 159 PHE cc_start: 0.7081 (m-80) cc_final: 0.6871 (m-80) REVERT: I 174 THR cc_start: 0.6286 (p) cc_final: 0.6049 (p) REVERT: J 55 TYR cc_start: 0.6956 (p90) cc_final: 0.6527 (p90) REVERT: L 8 MET cc_start: 0.7273 (mtt) cc_final: 0.6559 (mtm) REVERT: L 184 MET cc_start: 0.7762 (mmm) cc_final: 0.7090 (tpp) REVERT: M 104 MET cc_start: 0.1953 (tpp) cc_final: 0.1654 (tpp) REVERT: N 60 VAL cc_start: 0.4922 (t) cc_final: 0.4213 (t) REVERT: N 131 GLU cc_start: 0.6883 (pm20) cc_final: 0.6642 (pm20) REVERT: O 85 ARG cc_start: 0.6371 (ttt-90) cc_final: 0.6066 (ttt-90) REVERT: O 91 LYS cc_start: 0.5313 (mmtm) cc_final: 0.5024 (mmtt) REVERT: O 118 MET cc_start: 0.5498 (mmp) cc_final: 0.4736 (mtt) REVERT: O 171 LYS cc_start: 0.2851 (tttt) cc_final: 0.2215 (tptt) REVERT: P 110 ASP cc_start: 0.8773 (p0) cc_final: 0.8036 (t0) REVERT: P 152 GLU cc_start: 0.6221 (mt-10) cc_final: 0.5524 (mt-10) REVERT: Q 34 PHE cc_start: 0.6136 (t80) cc_final: 0.5845 (t80) REVERT: Q 70 MET cc_start: 0.5140 (mmm) cc_final: 0.4938 (mmm) REVERT: Q 76 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5523 (mp0) REVERT: Q 87 THR cc_start: 0.7942 (p) cc_final: 0.7146 (t) REVERT: Q 151 HIS cc_start: 0.6827 (m-70) cc_final: 0.6558 (m-70) REVERT: R 89 MET cc_start: 0.5929 (tpt) cc_final: 0.5420 (tpt) REVERT: R 97 ARG cc_start: 0.5449 (mtt-85) cc_final: 0.5158 (ttp80) REVERT: S 28 TYR cc_start: 0.4903 (m-80) cc_final: 0.4352 (m-80) REVERT: T 52 MET cc_start: 0.6701 (tpt) cc_final: 0.6462 (mmm) REVERT: T 159 MET cc_start: 0.6984 (pmm) cc_final: 0.6334 (pmm) REVERT: V 50 ASN cc_start: 0.8439 (m-40) cc_final: 0.7982 (t0) REVERT: V 86 LYS cc_start: 0.7864 (tptt) cc_final: 0.7553 (tptm) REVERT: X 68 ARG cc_start: 0.6071 (ptt90) cc_final: 0.5252 (ptt-90) REVERT: X 109 ILE cc_start: 0.7658 (mt) cc_final: 0.7309 (mt) REVERT: X 124 VAL cc_start: 0.8698 (t) cc_final: 0.8421 (m) REVERT: Y 10 ASP cc_start: 0.7516 (t70) cc_final: 0.7295 (m-30) REVERT: Y 59 ARG cc_start: 0.4421 (mmt90) cc_final: 0.3942 (mtp-110) REVERT: Y 70 VAL cc_start: 0.7635 (t) cc_final: 0.7223 (m) REVERT: Z 46 ILE cc_start: 0.5913 (pt) cc_final: 0.5587 (pt) REVERT: a 58 MET cc_start: 0.2579 (mtm) cc_final: 0.1494 (tpt) REVERT: b 57 MET cc_start: 0.2933 (ttm) cc_final: 0.1876 (tpt) REVERT: c 22 MET cc_start: 0.7115 (mmp) cc_final: 0.6690 (mmp) REVERT: c 81 LEU cc_start: 0.6683 (tp) cc_final: 0.6395 (tp) REVERT: d 44 ARG cc_start: 0.7034 (mmm-85) cc_final: 0.6055 (mmm-85) REVERT: d 67 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8358 (mmp80) REVERT: d 93 ASN cc_start: 0.6951 (t0) cc_final: 0.6484 (t0) REVERT: d 96 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6813 (mp0) REVERT: e 69 MET cc_start: 0.7106 (ppp) cc_final: 0.6504 (ttp) REVERT: f 104 MET cc_start: 0.4234 (mmm) cc_final: 0.3566 (mtt) REVERT: g 18 ASN cc_start: 0.8165 (t0) cc_final: 0.7544 (t0) REVERT: g 104 VAL cc_start: 0.7442 (t) cc_final: 0.7217 (t) REVERT: h 22 ASP cc_start: 0.5659 (t0) cc_final: 0.5392 (t0) REVERT: h 25 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7609 (mtmt) REVERT: h 117 ARG cc_start: 0.5926 (mtp180) cc_final: 0.5713 (mtp180) REVERT: i 58 MET cc_start: 0.4818 (mmm) cc_final: 0.3985 (ppp) REVERT: i 82 ARG cc_start: 0.4246 (mtt180) cc_final: 0.3995 (mtt90) REVERT: l 46 ARG cc_start: 0.8430 (ptt-90) cc_final: 0.8228 (ptp90) REVERT: l 49 LEU cc_start: 0.8768 (mm) cc_final: 0.8228 (mt) REVERT: n 12 ARG cc_start: 0.5479 (mtt180) cc_final: 0.5209 (mtt-85) REVERT: n 14 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8246 (mmtt) REVERT: r 49 VAL cc_start: 0.6656 (t) cc_final: 0.6011 (t) REVERT: s 101 MET cc_start: 0.1723 (tmm) cc_final: 0.1013 (ptp) REVERT: x 34 TRP cc_start: 0.8594 (m100) cc_final: 0.8226 (m-10) REVERT: x 54 MET cc_start: 0.8487 (mmp) cc_final: 0.8129 (mmp) REVERT: x 91 MET cc_start: 0.8397 (ttt) cc_final: 0.6923 (ttt) REVERT: x 163 LEU cc_start: 0.9392 (mt) cc_final: 0.8902 (mt) REVERT: x 166 ASP cc_start: 0.9197 (m-30) cc_final: 0.8894 (m-30) REVERT: x 171 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8183 (ptmm) REVERT: x 392 LYS cc_start: 0.9192 (mttp) cc_final: 0.8958 (mmtp) REVERT: x 407 THR cc_start: 0.8039 (t) cc_final: 0.7400 (t) REVERT: x 460 ILE cc_start: 0.9320 (mm) cc_final: 0.8884 (tt) REVERT: y 35 LYS cc_start: 0.8604 (tptt) cc_final: 0.8348 (tptp) REVERT: y 38 MET cc_start: 0.7544 (ttp) cc_final: 0.7239 (mmt) REVERT: z 76 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7655 (tpt) REVERT: z 89 ILE cc_start: 0.8900 (mm) cc_final: 0.8574 (tp) REVERT: 1 455 ILE cc_start: 0.9249 (mt) cc_final: 0.9026 (mt) REVERT: 3 42 PHE cc_start: 0.9126 (p90) cc_final: 0.8846 (p90) REVERT: 3 85 MET cc_start: 0.7986 (tmm) cc_final: 0.7741 (tmm) REVERT: 3 86 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: 3 94 PHE cc_start: 0.8807 (m-10) cc_final: 0.8527 (m-80) REVERT: 4 12 ASN cc_start: 0.8806 (m110) cc_final: 0.8587 (m110) REVERT: 4 14 LEU cc_start: 0.9551 (tt) cc_final: 0.9308 (tt) REVERT: 5 1 MET cc_start: -0.0790 (ttp) cc_final: -0.2447 (mtm) REVERT: 5 25 MET cc_start: 0.8993 (ptt) cc_final: 0.8692 (ppp) REVERT: 5 78 TYR cc_start: 0.8821 (t80) cc_final: 0.8373 (t80) REVERT: 5 114 ASN cc_start: 0.8835 (m110) cc_final: 0.7551 (m110) REVERT: 5 118 PHE cc_start: 0.8619 (m-10) cc_final: 0.7891 (m-10) REVERT: 5 145 LEU cc_start: 0.9476 (mt) cc_final: 0.9157 (mp) REVERT: 5 182 MET cc_start: 0.8459 (mmp) cc_final: 0.7929 (mmt) REVERT: 5 192 ILE cc_start: 0.8656 (mm) cc_final: 0.8445 (mm) REVERT: 5 198 CYS cc_start: 0.6998 (m) cc_final: 0.5393 (m) REVERT: 5 205 MET cc_start: 0.9309 (ttt) cc_final: 0.8571 (ttt) REVERT: 5 268 MET cc_start: 0.7284 (mtt) cc_final: 0.6536 (mtt) REVERT: 5 361 TYR cc_start: 0.8278 (t80) cc_final: 0.7536 (t80) REVERT: 5 367 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9319 (tt) REVERT: 5 373 VAL cc_start: 0.9395 (t) cc_final: 0.9047 (t) REVERT: 5 378 CYS cc_start: 0.9608 (m) cc_final: 0.9276 (m) REVERT: 5 398 TYR cc_start: 0.8868 (t80) cc_final: 0.8635 (t80) REVERT: 5 406 LEU cc_start: 0.9400 (tp) cc_final: 0.8954 (tp) REVERT: 5 414 MET cc_start: 0.8901 (mmt) cc_final: 0.8577 (mmt) REVERT: 5 469 ILE cc_start: 0.9315 (pt) cc_final: 0.8976 (tp) REVERT: 5 511 TRP cc_start: 0.7117 (t60) cc_final: 0.6568 (m100) outliers start: 36 outliers final: 6 residues processed: 1773 average time/residue: 1.4743 time to fit residues: 4446.3922 Evaluate side-chains 1319 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1309 time to evaluate : 7.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 622 optimal weight: 9.9990 chunk 347 optimal weight: 6.9990 chunk 931 optimal weight: 10.0000 chunk 762 optimal weight: 20.0000 chunk 308 optimal weight: 5.9990 chunk 1121 optimal weight: 7.9990 chunk 1211 optimal weight: 2.9990 chunk 998 optimal weight: 9.9990 chunk 1112 optimal weight: 0.9990 chunk 382 optimal weight: 7.9990 chunk 899 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN D 198 HIS D 244 HIS ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 128 ASN G 64 GLN G 66 GLN G 85 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN I 100 ASN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN L 13 HIS L 28 GLN L 104 ASN M 20 HIS ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN O 184 ASN ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN P 97 ASN Q 45 GLN ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS T 139 HIS U 50 ASN ** W 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 HIS ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN f 80 ASN h 20 GLN h 107 GLN i 15 HIS j 76 HIS ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN p 56 HIS s 41 GLN t 65 GLN x 72 ASN x 186 ASN x 238 ASN ** x 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 70 ASN ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 165109 Z= 0.325 Angle : 0.855 23.092 242524 Z= 0.434 Chirality : 0.045 0.317 30251 Planarity : 0.007 0.133 15718 Dihedral : 25.638 179.910 73507 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.77 % Allowed : 8.39 % Favored : 90.85 % Rotamer: Outliers : 0.42 % Allowed : 6.36 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.09), residues: 8227 helix: -0.31 (0.09), residues: 3237 sheet: -1.94 (0.15), residues: 956 loop : -2.12 (0.09), residues: 4034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP S 45 HIS 0.021 0.002 HIS x 404 PHE 0.036 0.003 PHE 5 256 TYR 0.041 0.003 TYR C 161 ARG 0.019 0.001 ARG Q 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1620 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1591 time to evaluate : 7.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7837 (mtt90) cc_final: 0.7500 (ttt180) REVERT: B 69 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7360 (mtmm) REVERT: B 81 THR cc_start: 0.2993 (p) cc_final: 0.2515 (p) REVERT: B 211 PHE cc_start: 0.4724 (m-10) cc_final: 0.4311 (m-10) REVERT: B 363 ILE cc_start: 0.5953 (mp) cc_final: 0.5218 (mp) REVERT: C 65 GLU cc_start: 0.9043 (tp30) cc_final: 0.8699 (pt0) REVERT: C 101 MET cc_start: 0.5710 (ptm) cc_final: 0.5412 (ptm) REVERT: D 207 TYR cc_start: 0.6033 (t80) cc_final: 0.5220 (t80) REVERT: D 208 MET cc_start: 0.5691 (ttm) cc_final: 0.5270 (ttm) REVERT: D 242 LYS cc_start: 0.9122 (pttm) cc_final: 0.8920 (mmtt) REVERT: D 275 GLN cc_start: 0.6650 (mt0) cc_final: 0.5783 (mm-40) REVERT: D 284 LYS cc_start: 0.5996 (mmtt) cc_final: 0.5782 (mmtt) REVERT: D 287 PHE cc_start: 0.7475 (m-80) cc_final: 0.7172 (m-80) REVERT: E 163 GLN cc_start: 0.5486 (tp40) cc_final: 0.4368 (tm-30) REVERT: F 76 MET cc_start: 0.8240 (tmm) cc_final: 0.7700 (tmm) REVERT: G 165 GLU cc_start: 0.6930 (mp0) cc_final: 0.6693 (mp0) REVERT: H 60 TRP cc_start: 0.4955 (m-90) cc_final: 0.4271 (m-90) REVERT: H 120 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7106 (mt-10) REVERT: I 56 GLU cc_start: 0.5366 (tp30) cc_final: 0.5025 (mm-30) REVERT: I 146 GLU cc_start: 0.7328 (pm20) cc_final: 0.6979 (pm20) REVERT: J 28 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7655 (mm-30) REVERT: J 99 PHE cc_start: 0.6426 (m-80) cc_final: 0.6092 (m-80) REVERT: L 8 MET cc_start: 0.7324 (mtt) cc_final: 0.6090 (mtp) REVERT: L 173 GLU cc_start: 0.7894 (pt0) cc_final: 0.7511 (tp30) REVERT: L 184 MET cc_start: 0.7605 (mmm) cc_final: 0.7189 (tpt) REVERT: M 113 MET cc_start: 0.7214 (ppp) cc_final: 0.6857 (ppp) REVERT: M 129 LYS cc_start: 0.6525 (mttt) cc_final: 0.5590 (tptt) REVERT: N 161 MET cc_start: 0.7513 (mmp) cc_final: 0.7115 (mmt) REVERT: N 189 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7412 (ttm170) REVERT: O 85 ARG cc_start: 0.6086 (ttt-90) cc_final: 0.5648 (ttt-90) REVERT: O 118 MET cc_start: 0.5793 (mmp) cc_final: 0.4872 (mtt) REVERT: O 171 LYS cc_start: 0.2970 (tttt) cc_final: 0.2614 (mtmt) REVERT: O 186 GLU cc_start: 0.4090 (mm-30) cc_final: 0.3534 (tp30) REVERT: P 28 ASN cc_start: 0.7581 (m110) cc_final: 0.7379 (m-40) REVERT: P 39 MET cc_start: 0.5807 (tpt) cc_final: 0.5594 (tpp) REVERT: P 91 LEU cc_start: 0.8608 (pp) cc_final: 0.8330 (pp) REVERT: Q 17 GLU cc_start: 0.6610 (mp0) cc_final: 0.6266 (mp0) REVERT: R 89 MET cc_start: 0.5987 (tpt) cc_final: 0.5764 (tpt) REVERT: R 97 ARG cc_start: 0.5945 (mtt-85) cc_final: 0.5616 (ttp80) REVERT: R 119 MET cc_start: 0.4369 (tpp) cc_final: 0.4076 (mtp) REVERT: S 27 LEU cc_start: 0.7925 (tt) cc_final: 0.7689 (tt) REVERT: T 31 MET cc_start: 0.6725 (mpp) cc_final: 0.5573 (mpp) REVERT: T 45 MET cc_start: 0.6968 (mtt) cc_final: 0.6696 (mtt) REVERT: X 109 ILE cc_start: 0.7837 (mt) cc_final: 0.7558 (mt) REVERT: Y 14 ASN cc_start: 0.8699 (m-40) cc_final: 0.7796 (t0) REVERT: Y 70 VAL cc_start: 0.7911 (t) cc_final: 0.7461 (m) REVERT: a 10 LYS cc_start: 0.7527 (mmtp) cc_final: 0.7196 (mmtp) REVERT: a 58 MET cc_start: 0.3136 (mtm) cc_final: 0.2307 (tpt) REVERT: b 43 MET cc_start: 0.4868 (tpt) cc_final: 0.4512 (tpt) REVERT: b 57 MET cc_start: 0.2950 (ttm) cc_final: 0.2062 (tpt) REVERT: d 67 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8120 (mmp80) REVERT: e 69 MET cc_start: 0.7370 (ppp) cc_final: 0.7007 (ttp) REVERT: f 104 MET cc_start: 0.3762 (mmm) cc_final: 0.3485 (mtt) REVERT: g 18 ASN cc_start: 0.8478 (t0) cc_final: 0.7996 (t0) REVERT: h 25 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7570 (mtmt) REVERT: i 58 MET cc_start: 0.4051 (mmm) cc_final: 0.3634 (ppp) REVERT: j 32 SER cc_start: 0.9345 (m) cc_final: 0.9006 (p) REVERT: k 47 ILE cc_start: 0.6518 (mm) cc_final: 0.6215 (mm) REVERT: k 54 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8319 (tp30) REVERT: l 46 ARG cc_start: 0.8679 (ptt-90) cc_final: 0.8420 (ptp90) REVERT: l 49 LEU cc_start: 0.8768 (mm) cc_final: 0.8399 (mt) REVERT: n 14 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8129 (mmtt) REVERT: o 8 ARG cc_start: 0.6914 (tpp-160) cc_final: 0.6523 (tpp-160) REVERT: r 49 VAL cc_start: 0.7430 (t) cc_final: 0.7063 (t) REVERT: s 95 LEU cc_start: -0.1024 (pp) cc_final: -0.1271 (pt) REVERT: s 101 MET cc_start: 0.1878 (tmm) cc_final: 0.1207 (ptm) REVERT: x 34 TRP cc_start: 0.8620 (m100) cc_final: 0.8195 (m-10) REVERT: x 54 MET cc_start: 0.8598 (mmp) cc_final: 0.8332 (mmm) REVERT: x 163 LEU cc_start: 0.9270 (mt) cc_final: 0.9050 (mt) REVERT: x 167 GLU cc_start: 0.8771 (mt-10) cc_final: 0.7680 (tm-30) REVERT: x 171 LYS cc_start: 0.8908 (mtmt) cc_final: 0.8202 (ttpp) REVERT: x 401 MET cc_start: 0.8250 (mmm) cc_final: 0.7881 (mmm) REVERT: x 431 LEU cc_start: 0.9172 (tp) cc_final: 0.8881 (tp) REVERT: x 453 ILE cc_start: 0.9276 (mt) cc_final: 0.9071 (mt) REVERT: y 38 MET cc_start: 0.7232 (ttp) cc_final: 0.6758 (mmt) REVERT: z 89 ILE cc_start: 0.8914 (mm) cc_final: 0.8690 (mm) REVERT: 1 455 ILE cc_start: 0.9331 (mt) cc_final: 0.9106 (mt) REVERT: 3 90 SER cc_start: 0.8863 (m) cc_final: 0.8248 (m) REVERT: 3 94 PHE cc_start: 0.8937 (m-10) cc_final: 0.8694 (m-80) REVERT: 4 12 ASN cc_start: 0.8932 (m110) cc_final: 0.8668 (m110) REVERT: 5 1 MET cc_start: -0.0849 (ttp) cc_final: -0.2553 (mtm) REVERT: 5 78 TYR cc_start: 0.8933 (t80) cc_final: 0.8315 (t80) REVERT: 5 114 ASN cc_start: 0.8839 (m110) cc_final: 0.8206 (m-40) REVERT: 5 192 ILE cc_start: 0.8627 (mm) cc_final: 0.8281 (mt) REVERT: 5 227 MET cc_start: 0.8383 (tmm) cc_final: 0.8044 (tmm) REVERT: 5 228 LEU cc_start: 0.9576 (mt) cc_final: 0.9247 (mt) REVERT: 5 278 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8070 (tm-30) REVERT: 5 361 TYR cc_start: 0.8469 (t80) cc_final: 0.7835 (t80) REVERT: 5 378 CYS cc_start: 0.9374 (m) cc_final: 0.9172 (m) REVERT: 5 406 LEU cc_start: 0.9314 (tp) cc_final: 0.9033 (tp) REVERT: 5 461 ILE cc_start: 0.9138 (mt) cc_final: 0.8910 (mt) REVERT: 5 469 ILE cc_start: 0.9358 (pt) cc_final: 0.9086 (tp) REVERT: 5 511 TRP cc_start: 0.7136 (t60) cc_final: 0.6546 (m100) REVERT: 5 568 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8604 (mm-30) REVERT: 5 599 MET cc_start: 0.9102 (mpp) cc_final: 0.8764 (mpp) REVERT: 5 688 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7521 (tt) outliers start: 29 outliers final: 10 residues processed: 1610 average time/residue: 1.4111 time to fit residues: 3878.4304 Evaluate side-chains 1245 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1234 time to evaluate : 7.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 1108 optimal weight: 0.6980 chunk 843 optimal weight: 20.0000 chunk 582 optimal weight: 0.0040 chunk 124 optimal weight: 3.9990 chunk 535 optimal weight: 10.0000 chunk 753 optimal weight: 50.0000 chunk 1125 optimal weight: 30.0000 chunk 1191 optimal weight: 8.9990 chunk 588 optimal weight: 10.0000 chunk 1066 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 overall best weight: 3.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN B 167 GLN B 179 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN C 41 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN D 244 HIS D 291 GLN F 101 ASN G 64 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 HIS ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 104 ASN M 33 GLN N 32 GLN ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 97 ASN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 HIS W 48 GLN ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 ASN ** a 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 HIS f 21 GLN f 80 ASN h 20 GLN j 76 HIS l 19 GLN ** m 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 ASN ** r 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 514 HIS 5 545 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 165109 Z= 0.252 Angle : 0.775 17.465 242524 Z= 0.390 Chirality : 0.042 0.309 30251 Planarity : 0.006 0.131 15718 Dihedral : 25.516 179.256 73507 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.33 % Favored : 91.93 % Rotamer: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.09), residues: 8227 helix: -0.05 (0.09), residues: 3271 sheet: -1.60 (0.16), residues: 937 loop : -1.97 (0.09), residues: 4019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP U 99 HIS 0.018 0.002 HIS x 404 PHE 0.055 0.003 PHE x 182 TYR 0.040 0.003 TYR C 161 ARG 0.019 0.001 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1574 time to evaluate : 9.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7562 (ttt180) REVERT: B 69 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7451 (mtmm) REVERT: B 78 ILE cc_start: 0.7298 (mp) cc_final: 0.7089 (mp) REVERT: B 81 THR cc_start: 0.2881 (p) cc_final: 0.2545 (p) REVERT: B 211 PHE cc_start: 0.4259 (m-80) cc_final: 0.3913 (m-10) REVERT: B 363 ILE cc_start: 0.5795 (mp) cc_final: 0.5270 (mp) REVERT: B 369 ASP cc_start: 0.5802 (t0) cc_final: 0.5532 (m-30) REVERT: C 65 GLU cc_start: 0.9075 (tp30) cc_final: 0.8704 (pt0) REVERT: C 95 MET cc_start: 0.8334 (pmm) cc_final: 0.8131 (pmm) REVERT: C 101 MET cc_start: 0.5688 (ptm) cc_final: 0.4456 (tpt) REVERT: C 217 ILE cc_start: 0.3432 (tp) cc_final: 0.3093 (tp) REVERT: C 284 MET cc_start: 0.5487 (ptm) cc_final: 0.4601 (tmm) REVERT: C 303 ARG cc_start: 0.4104 (pmt-80) cc_final: 0.3858 (ptt-90) REVERT: D 207 TYR cc_start: 0.6126 (t80) cc_final: 0.5354 (t80) REVERT: D 242 LYS cc_start: 0.9116 (pttm) cc_final: 0.8869 (mmtm) REVERT: D 275 GLN cc_start: 0.6898 (mt0) cc_final: 0.6094 (mm-40) REVERT: D 287 PHE cc_start: 0.7288 (m-80) cc_final: 0.6979 (m-80) REVERT: E 163 GLN cc_start: 0.5654 (tp40) cc_final: 0.4391 (tm-30) REVERT: F 76 MET cc_start: 0.8201 (tmm) cc_final: 0.7845 (tmm) REVERT: H 60 TRP cc_start: 0.4989 (m-90) cc_final: 0.4282 (m-90) REVERT: I 56 GLU cc_start: 0.4842 (tp30) cc_final: 0.4626 (mm-30) REVERT: I 115 MET cc_start: 0.7551 (ttm) cc_final: 0.7342 (ttm) REVERT: J 163 MET cc_start: 0.5991 (mmm) cc_final: 0.5323 (mmp) REVERT: L 8 MET cc_start: 0.7156 (mtt) cc_final: 0.5900 (mtp) REVERT: L 173 GLU cc_start: 0.7801 (pt0) cc_final: 0.7464 (tp30) REVERT: L 184 MET cc_start: 0.7569 (mmm) cc_final: 0.7130 (tpt) REVERT: M 104 MET cc_start: 0.2147 (tpp) cc_final: 0.0782 (tpp) REVERT: M 129 LYS cc_start: 0.6639 (mttt) cc_final: 0.5653 (tptt) REVERT: N 161 MET cc_start: 0.7562 (mmp) cc_final: 0.5882 (mmt) REVERT: N 189 ARG cc_start: 0.7712 (ttm110) cc_final: 0.7433 (ttm170) REVERT: O 87 MET cc_start: 0.6302 (mpp) cc_final: 0.5686 (mpp) REVERT: O 171 LYS cc_start: 0.2944 (tttt) cc_final: 0.2448 (mtmt) REVERT: O 186 GLU cc_start: 0.4374 (mm-30) cc_final: 0.3837 (tp30) REVERT: P 82 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7874 (mtt-85) REVERT: P 151 THR cc_start: 0.5905 (m) cc_final: 0.5658 (m) REVERT: Q 87 THR cc_start: 0.8091 (p) cc_final: 0.7651 (p) REVERT: R 89 MET cc_start: 0.5845 (tpt) cc_final: 0.5399 (ptp) REVERT: R 97 ARG cc_start: 0.5825 (mtt-85) cc_final: 0.5450 (ttp80) REVERT: R 126 LYS cc_start: 0.7394 (ptpp) cc_final: 0.7189 (ptpp) REVERT: S 12 VAL cc_start: 0.7507 (p) cc_final: 0.7158 (t) REVERT: S 52 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7874 (mmtt) REVERT: T 31 MET cc_start: 0.6661 (mpp) cc_final: 0.5668 (mpp) REVERT: U 73 THR cc_start: 0.7293 (m) cc_final: 0.6938 (p) REVERT: W 50 ASN cc_start: 0.5833 (m110) cc_final: 0.5428 (t0) REVERT: Y 14 ASN cc_start: 0.8800 (m110) cc_final: 0.7795 (t0) REVERT: Y 70 VAL cc_start: 0.7643 (t) cc_final: 0.7122 (m) REVERT: Y 73 VAL cc_start: 0.6614 (t) cc_final: 0.6356 (t) REVERT: Y 83 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7869 (mt-10) REVERT: Z 73 LYS cc_start: 0.6185 (mmtt) cc_final: 0.5510 (mtpp) REVERT: Z 92 ASP cc_start: 0.7335 (p0) cc_final: 0.7013 (p0) REVERT: a 10 LYS cc_start: 0.7126 (mmtp) cc_final: 0.6740 (mmtp) REVERT: b 43 MET cc_start: 0.4975 (tpt) cc_final: 0.4684 (tpt) REVERT: b 57 MET cc_start: 0.2954 (ttm) cc_final: 0.2139 (tpt) REVERT: b 65 MET cc_start: 0.6680 (mmp) cc_final: 0.5970 (tmm) REVERT: d 67 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8059 (mmp80) REVERT: e 48 ARG cc_start: 0.6909 (mtt180) cc_final: 0.6610 (mtt180) REVERT: e 69 MET cc_start: 0.7310 (ppp) cc_final: 0.6991 (ttp) REVERT: g 18 ASN cc_start: 0.8319 (t0) cc_final: 0.7932 (t0) REVERT: g 100 GLN cc_start: 0.6501 (tm-30) cc_final: 0.6246 (tm-30) REVERT: h 25 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7633 (mtpt) REVERT: i 58 MET cc_start: 0.4505 (mmm) cc_final: 0.3984 (ppp) REVERT: j 32 SER cc_start: 0.9385 (m) cc_final: 0.9021 (p) REVERT: k 55 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8842 (ptpp) REVERT: l 17 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8525 (tm-30) REVERT: l 26 TRP cc_start: 0.8646 (p-90) cc_final: 0.7190 (p-90) REVERT: l 46 ARG cc_start: 0.8721 (ptt-90) cc_final: 0.8507 (ptp90) REVERT: n 2 ARG cc_start: 0.6251 (ttt180) cc_final: 0.5132 (mtm180) REVERT: n 14 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8002 (mmtt) REVERT: s 101 MET cc_start: 0.1507 (tmm) cc_final: 0.0923 (ptp) REVERT: x 33 LEU cc_start: 0.9147 (tt) cc_final: 0.8904 (tt) REVERT: x 34 TRP cc_start: 0.8707 (m100) cc_final: 0.8223 (m-10) REVERT: x 160 LEU cc_start: 0.9008 (mt) cc_final: 0.8662 (mt) REVERT: x 163 LEU cc_start: 0.9335 (mt) cc_final: 0.9119 (mt) REVERT: x 166 ASP cc_start: 0.9175 (m-30) cc_final: 0.8712 (m-30) REVERT: x 167 GLU cc_start: 0.8781 (mt-10) cc_final: 0.7478 (tm-30) REVERT: x 171 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8120 (ttpp) REVERT: x 294 GLN cc_start: 0.9092 (mt0) cc_final: 0.8751 (mt0) REVERT: x 406 GLU cc_start: 0.8110 (pp20) cc_final: 0.7585 (pp20) REVERT: x 431 LEU cc_start: 0.9188 (tp) cc_final: 0.8942 (tp) REVERT: x 453 ILE cc_start: 0.9242 (mt) cc_final: 0.9016 (mt) REVERT: y 38 MET cc_start: 0.6972 (ttp) cc_final: 0.6591 (mmt) REVERT: z 85 PHE cc_start: 0.7812 (t80) cc_final: 0.7603 (t80) REVERT: 1 451 PHE cc_start: 0.8156 (t80) cc_final: 0.7951 (t80) REVERT: 1 455 ILE cc_start: 0.9301 (mt) cc_final: 0.9058 (mt) REVERT: 3 90 SER cc_start: 0.8752 (m) cc_final: 0.8087 (m) REVERT: 3 94 PHE cc_start: 0.8911 (m-10) cc_final: 0.8619 (m-80) REVERT: 4 12 ASN cc_start: 0.8918 (m110) cc_final: 0.8653 (m110) REVERT: 4 14 LEU cc_start: 0.9488 (tt) cc_final: 0.9254 (tt) REVERT: 4 18 LEU cc_start: 0.9227 (tt) cc_final: 0.8888 (tt) REVERT: 5 1 MET cc_start: -0.0837 (ttp) cc_final: -0.2628 (mtm) REVERT: 5 78 TYR cc_start: 0.8909 (t80) cc_final: 0.8189 (t80) REVERT: 5 114 ASN cc_start: 0.8801 (m110) cc_final: 0.7379 (m110) REVERT: 5 118 PHE cc_start: 0.8477 (m-10) cc_final: 0.7944 (m-10) REVERT: 5 145 LEU cc_start: 0.9533 (mt) cc_final: 0.9325 (mp) REVERT: 5 182 MET cc_start: 0.8400 (mmp) cc_final: 0.7870 (mmt) REVERT: 5 198 CYS cc_start: 0.6829 (m) cc_final: 0.5745 (m) REVERT: 5 227 MET cc_start: 0.8117 (tmm) cc_final: 0.7852 (tmm) REVERT: 5 228 LEU cc_start: 0.9542 (mt) cc_final: 0.9191 (mt) REVERT: 5 268 MET cc_start: 0.7333 (mtt) cc_final: 0.6557 (mtt) REVERT: 5 278 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7981 (tm-30) REVERT: 5 357 TRP cc_start: 0.9135 (p-90) cc_final: 0.8848 (p-90) REVERT: 5 361 TYR cc_start: 0.8319 (t80) cc_final: 0.7967 (t80) REVERT: 5 406 LEU cc_start: 0.9326 (tp) cc_final: 0.9091 (tp) REVERT: 5 418 SER cc_start: 0.9400 (m) cc_final: 0.8484 (m) REVERT: 5 461 ILE cc_start: 0.9225 (mt) cc_final: 0.8881 (mt) REVERT: 5 469 ILE cc_start: 0.9418 (pt) cc_final: 0.9121 (tp) REVERT: 5 511 TRP cc_start: 0.7243 (t60) cc_final: 0.6569 (m100) REVERT: 5 514 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7526 (t-90) REVERT: 5 523 MET cc_start: 0.7841 (ttt) cc_final: 0.7461 (mtp) REVERT: 5 568 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8632 (mm-30) REVERT: 5 599 MET cc_start: 0.9094 (mpp) cc_final: 0.8793 (mpp) REVERT: 5 640 TYR cc_start: 0.6066 (t80) cc_final: 0.5663 (t80) REVERT: 5 664 ARG cc_start: 0.7474 (mpp-170) cc_final: 0.7165 (mtm-85) outliers start: 9 outliers final: 0 residues processed: 1579 average time/residue: 1.4078 time to fit residues: 3805.1260 Evaluate side-chains 1233 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1232 time to evaluate : 7.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 992 optimal weight: 10.0000 chunk 676 optimal weight: 10.0000 chunk 17 optimal weight: 0.0270 chunk 887 optimal weight: 10.0000 chunk 491 optimal weight: 3.9990 chunk 1017 optimal weight: 30.0000 chunk 823 optimal weight: 40.0000 chunk 1 optimal weight: 2.9990 chunk 608 optimal weight: 10.0000 chunk 1069 optimal weight: 2.9990 chunk 300 optimal weight: 0.0570 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS C 343 GLN D 244 HIS D 291 GLN E 223 HIS G 64 GLN H 42 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 104 ASN ** N 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 180 GLN O 184 ASN P 28 ASN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN R 34 ASN R 130 ASN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS U 94 ASN W 17 HIS ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 ASN Y 56 GLN a 19 HIS ** a 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 GLN ** j 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN ** m 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 GLN t 95 GLN ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 397 GLN ** x 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 12 ASN ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 424 GLN ** 5 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 165109 Z= 0.192 Angle : 0.704 18.827 242524 Z= 0.357 Chirality : 0.039 0.294 30251 Planarity : 0.005 0.125 15718 Dihedral : 25.394 179.456 73507 Min Nonbonded Distance : 1.485 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.24 % Favored : 92.05 % Rotamer: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 8227 helix: 0.26 (0.09), residues: 3246 sheet: -1.38 (0.16), residues: 934 loop : -1.83 (0.09), residues: 4047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 196 HIS 0.025 0.001 HIS x 404 PHE 0.054 0.002 PHE x 182 TYR 0.035 0.002 TYR p 18 ARG 0.015 0.001 ARG o 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1557 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1550 time to evaluate : 7.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.7751 (mpt180) cc_final: 0.7202 (mpt180) REVERT: B 50 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7476 (mmmm) REVERT: B 69 LYS cc_start: 0.7757 (mmtm) cc_final: 0.7291 (mtmm) REVERT: B 90 VAL cc_start: 0.7293 (p) cc_final: 0.6818 (p) REVERT: B 211 PHE cc_start: 0.4419 (m-80) cc_final: 0.3973 (m-10) REVERT: C 65 GLU cc_start: 0.9030 (tp30) cc_final: 0.8615 (pt0) REVERT: C 101 MET cc_start: 0.5572 (ptm) cc_final: 0.4286 (tpt) REVERT: C 303 ARG cc_start: 0.4423 (pmt-80) cc_final: 0.4083 (ptt-90) REVERT: C 341 LEU cc_start: 0.7529 (pp) cc_final: 0.6196 (tp) REVERT: D 115 MET cc_start: 0.7171 (ptm) cc_final: 0.6838 (ttm) REVERT: D 207 TYR cc_start: 0.6039 (t80) cc_final: 0.5274 (t80) REVERT: D 208 MET cc_start: 0.5971 (ttm) cc_final: 0.5552 (ttm) REVERT: D 242 LYS cc_start: 0.9093 (pttm) cc_final: 0.8819 (mmtm) REVERT: D 275 GLN cc_start: 0.6955 (mt0) cc_final: 0.6047 (mm-40) REVERT: E 163 GLN cc_start: 0.5464 (tp40) cc_final: 0.4350 (tm-30) REVERT: H 92 MET cc_start: 0.3207 (tpt) cc_final: 0.2431 (tpt) REVERT: H 120 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6908 (mt-10) REVERT: H 128 MET cc_start: 0.4857 (mmt) cc_final: 0.4638 (mmt) REVERT: I 3 ARG cc_start: 0.7072 (ptp-170) cc_final: 0.6581 (ptt90) REVERT: I 146 GLU cc_start: 0.7475 (pm20) cc_final: 0.7168 (pm20) REVERT: L 8 MET cc_start: 0.7280 (mtt) cc_final: 0.6253 (ttm) REVERT: L 173 GLU cc_start: 0.7728 (pt0) cc_final: 0.7428 (tp30) REVERT: L 184 MET cc_start: 0.7410 (mmm) cc_final: 0.6979 (tpp) REVERT: M 104 MET cc_start: 0.2871 (tpp) cc_final: 0.2151 (tpp) REVERT: M 113 MET cc_start: 0.7030 (ppp) cc_final: 0.6688 (ppp) REVERT: M 129 LYS cc_start: 0.6576 (mttt) cc_final: 0.5676 (tptt) REVERT: N 161 MET cc_start: 0.7370 (mmp) cc_final: 0.6836 (mmp) REVERT: O 87 MET cc_start: 0.6211 (mpp) cc_final: 0.5960 (mpp) REVERT: O 118 MET cc_start: 0.5850 (mpp) cc_final: 0.5418 (mtt) REVERT: O 171 LYS cc_start: 0.2843 (tttt) cc_final: 0.2505 (mtmt) REVERT: O 186 GLU cc_start: 0.3964 (mm-30) cc_final: 0.3726 (tp30) REVERT: P 29 THR cc_start: 0.8341 (t) cc_final: 0.8107 (m) REVERT: Q 17 GLU cc_start: 0.7096 (mp0) cc_final: 0.6425 (tt0) REVERT: Q 87 THR cc_start: 0.8158 (p) cc_final: 0.7775 (p) REVERT: R 89 MET cc_start: 0.5827 (tpt) cc_final: 0.5439 (ptm) REVERT: R 97 ARG cc_start: 0.5664 (mtt-85) cc_final: 0.5353 (ttp80) REVERT: S 52 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7906 (mmtt) REVERT: T 31 MET cc_start: 0.6460 (mpp) cc_final: 0.5311 (mpp) REVERT: T 48 VAL cc_start: 0.8776 (t) cc_final: 0.8167 (t) REVERT: Y 14 ASN cc_start: 0.8103 (m110) cc_final: 0.7589 (t0) REVERT: Y 70 VAL cc_start: 0.7599 (t) cc_final: 0.7115 (m) REVERT: Y 132 LYS cc_start: 0.4622 (tmtt) cc_final: 0.3822 (mmtm) REVERT: Z 47 ASP cc_start: 0.6905 (t0) cc_final: 0.6661 (t70) REVERT: Z 73 LYS cc_start: 0.6217 (mmtt) cc_final: 0.5660 (mttp) REVERT: Z 92 ASP cc_start: 0.7278 (p0) cc_final: 0.6984 (p0) REVERT: a 10 LYS cc_start: 0.7066 (mmtp) cc_final: 0.6857 (mmtp) REVERT: a 77 LYS cc_start: 0.5308 (mttp) cc_final: 0.4764 (pttt) REVERT: b 43 MET cc_start: 0.5178 (tpt) cc_final: 0.4784 (tpt) REVERT: b 57 MET cc_start: 0.2968 (ttm) cc_final: 0.2249 (tpt) REVERT: b 65 MET cc_start: 0.6542 (mmp) cc_final: 0.5834 (tmm) REVERT: d 29 ILE cc_start: 0.7774 (mt) cc_final: 0.7487 (mt) REVERT: d 67 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8042 (mmp80) REVERT: e 69 MET cc_start: 0.7264 (ppp) cc_final: 0.6708 (ttp) REVERT: g 5 LEU cc_start: 0.8146 (pt) cc_final: 0.7644 (pt) REVERT: g 8 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7645 (ttm110) REVERT: g 18 ASN cc_start: 0.8411 (t0) cc_final: 0.7918 (t0) REVERT: g 32 TYR cc_start: 0.7787 (m-80) cc_final: 0.7587 (m-80) REVERT: g 100 GLN cc_start: 0.6499 (tm-30) cc_final: 0.6249 (tm-30) REVERT: h 25 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7653 (mtmt) REVERT: i 58 MET cc_start: 0.4356 (mmm) cc_final: 0.4074 (ppp) REVERT: j 32 SER cc_start: 0.9357 (m) cc_final: 0.8983 (p) REVERT: n 2 ARG cc_start: 0.6362 (ttt180) cc_final: 0.5098 (mtm180) REVERT: n 14 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7988 (mmtt) REVERT: r 8 MET cc_start: 0.3377 (mmp) cc_final: 0.3072 (mmt) REVERT: r 63 VAL cc_start: 0.6795 (t) cc_final: 0.6240 (t) REVERT: s 101 MET cc_start: 0.1575 (tmm) cc_final: 0.0691 (ptp) REVERT: x 33 LEU cc_start: 0.9173 (tt) cc_final: 0.8962 (tt) REVERT: x 34 TRP cc_start: 0.8696 (m100) cc_final: 0.8247 (m-10) REVERT: x 160 LEU cc_start: 0.9079 (mt) cc_final: 0.8710 (mt) REVERT: x 163 LEU cc_start: 0.9288 (mt) cc_final: 0.9067 (mt) REVERT: x 166 ASP cc_start: 0.9189 (m-30) cc_final: 0.8703 (m-30) REVERT: x 167 GLU cc_start: 0.8741 (mt-10) cc_final: 0.7351 (tm-30) REVERT: x 168 LEU cc_start: 0.8712 (mt) cc_final: 0.8477 (mt) REVERT: x 171 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8145 (ttpp) REVERT: x 392 LYS cc_start: 0.9429 (mmtm) cc_final: 0.9030 (mptt) REVERT: x 406 GLU cc_start: 0.8073 (pp20) cc_final: 0.7758 (pp20) REVERT: x 431 LEU cc_start: 0.9080 (tp) cc_final: 0.8871 (tp) REVERT: x 453 ILE cc_start: 0.9231 (mt) cc_final: 0.8990 (mt) REVERT: y 38 MET cc_start: 0.6848 (ttp) cc_final: 0.6527 (mmt) REVERT: 1 451 PHE cc_start: 0.8109 (t80) cc_final: 0.7858 (t80) REVERT: 1 455 ILE cc_start: 0.9316 (mt) cc_final: 0.9059 (mt) REVERT: 3 90 SER cc_start: 0.8753 (m) cc_final: 0.8064 (p) REVERT: 3 94 PHE cc_start: 0.8848 (m-10) cc_final: 0.8619 (m-80) REVERT: 4 12 ASN cc_start: 0.8875 (m-40) cc_final: 0.8558 (m110) REVERT: 5 1 MET cc_start: -0.0848 (ttp) cc_final: -0.2531 (mtm) REVERT: 5 35 LEU cc_start: 0.9633 (mt) cc_final: 0.9398 (mt) REVERT: 5 78 TYR cc_start: 0.8802 (t80) cc_final: 0.8202 (t80) REVERT: 5 114 ASN cc_start: 0.8755 (m110) cc_final: 0.7093 (m-40) REVERT: 5 118 PHE cc_start: 0.8513 (m-10) cc_final: 0.7715 (m-10) REVERT: 5 182 MET cc_start: 0.8374 (mmp) cc_final: 0.7758 (mmt) REVERT: 5 198 CYS cc_start: 0.6967 (m) cc_final: 0.6008 (m) REVERT: 5 252 MET cc_start: 0.8598 (mmt) cc_final: 0.8300 (mmm) REVERT: 5 278 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7981 (tm-30) REVERT: 5 361 TYR cc_start: 0.8130 (t80) cc_final: 0.7677 (t80) REVERT: 5 406 LEU cc_start: 0.9193 (tp) cc_final: 0.8987 (tp) REVERT: 5 418 SER cc_start: 0.9477 (m) cc_final: 0.9023 (p) REVERT: 5 424 GLN cc_start: 0.8919 (tp40) cc_final: 0.8635 (tp-100) REVERT: 5 431 LYS cc_start: 0.9105 (ptpp) cc_final: 0.8594 (pttt) REVERT: 5 469 ILE cc_start: 0.9394 (pt) cc_final: 0.9120 (tp) REVERT: 5 511 TRP cc_start: 0.7110 (t60) cc_final: 0.6665 (m100) REVERT: 5 525 TRP cc_start: 0.7377 (t-100) cc_final: 0.6335 (t-100) REVERT: 5 568 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8594 (mm-30) REVERT: 5 640 TYR cc_start: 0.5672 (t80) cc_final: 0.5235 (t80) REVERT: 5 664 ARG cc_start: 0.7441 (mpp-170) cc_final: 0.7044 (mtm-85) outliers start: 7 outliers final: 0 residues processed: 1555 average time/residue: 1.3840 time to fit residues: 3685.9444 Evaluate side-chains 1215 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1215 time to evaluate : 7.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 400 optimal weight: 6.9990 chunk 1073 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 699 optimal weight: 20.0000 chunk 294 optimal weight: 7.9990 chunk 1192 optimal weight: 10.0000 chunk 990 optimal weight: 5.9990 chunk 552 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 394 optimal weight: 10.0000 chunk 626 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS B 276 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN D 244 HIS D 291 GLN E 187 GLN G 64 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 HIS H 156 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN M 20 HIS M 56 GLN N 109 HIS ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 HIS O 90 HIS O 150 GLN O 184 ASN ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN P 118 GLN P 133 HIS R 66 ASN ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 125 GLN ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 HIS ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 GLN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 67 GLN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 13 ASN ** j 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN l 38 ASN ** m 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 ASN ** r 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 139 GLN ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 ASN ** x 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 397 GLN 5 101 HIS ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 165109 Z= 0.364 Angle : 0.873 22.164 242524 Z= 0.436 Chirality : 0.046 0.363 30251 Planarity : 0.007 0.141 15718 Dihedral : 25.533 179.877 73507 Min Nonbonded Distance : 1.009 Molprobity Statistics. All-atom Clashscore : 29.16 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.52 % Favored : 90.82 % Rotamer: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.09), residues: 8227 helix: -0.17 (0.09), residues: 3266 sheet: -1.39 (0.16), residues: 919 loop : -2.02 (0.09), residues: 4042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP S 45 HIS 0.029 0.002 HIS x 404 PHE 0.059 0.003 PHE x 182 TYR 0.035 0.003 TYR 5 100 ARG 0.027 0.001 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1501 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1494 time to evaluate : 7.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7566 (mmtt) REVERT: A 188 LYS cc_start: 0.8389 (tttm) cc_final: 0.8188 (tttm) REVERT: A 241 ARG cc_start: 0.7849 (mpt180) cc_final: 0.7551 (mpt180) REVERT: B 69 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7290 (mtmm) REVERT: B 78 ILE cc_start: 0.7076 (mp) cc_final: 0.6774 (mp) REVERT: B 81 THR cc_start: 0.3608 (p) cc_final: 0.3314 (p) REVERT: B 211 PHE cc_start: 0.4538 (m-80) cc_final: 0.4315 (m-80) REVERT: B 363 ILE cc_start: 0.6603 (mp) cc_final: 0.5773 (mp) REVERT: C 28 PHE cc_start: 0.6015 (m-80) cc_final: 0.5780 (m-80) REVERT: C 65 GLU cc_start: 0.9176 (tp30) cc_final: 0.8791 (pt0) REVERT: C 101 MET cc_start: 0.5945 (ptm) cc_final: 0.4655 (tpt) REVERT: C 161 TYR cc_start: 0.6428 (m-80) cc_final: 0.5488 (m-80) REVERT: C 284 MET cc_start: 0.5994 (ptm) cc_final: 0.5086 (tmm) REVERT: D 208 MET cc_start: 0.5503 (ttm) cc_final: 0.5211 (ttm) REVERT: D 242 LYS cc_start: 0.9132 (pttm) cc_final: 0.8889 (mmtt) REVERT: D 275 GLN cc_start: 0.7353 (mt0) cc_final: 0.6583 (mm-40) REVERT: D 287 PHE cc_start: 0.7663 (m-80) cc_final: 0.7380 (m-80) REVERT: E 187 GLN cc_start: 0.4994 (OUTLIER) cc_final: 0.4498 (pp30) REVERT: H 92 MET cc_start: 0.2882 (tpt) cc_final: 0.2268 (tpt) REVERT: H 128 MET cc_start: 0.5081 (mmt) cc_final: 0.4700 (mmt) REVERT: H 143 GLU cc_start: 0.5825 (tp30) cc_final: 0.5205 (tp30) REVERT: I 21 ARG cc_start: 0.8015 (ptm-80) cc_final: 0.7798 (ptt180) REVERT: I 56 GLU cc_start: 0.5309 (tp30) cc_final: 0.5071 (mm-30) REVERT: J 22 LEU cc_start: 0.5464 (mt) cc_final: 0.5045 (tt) REVERT: L 8 MET cc_start: 0.7196 (mtt) cc_final: 0.5921 (mtp) REVERT: L 173 GLU cc_start: 0.7770 (pt0) cc_final: 0.7271 (tp30) REVERT: L 184 MET cc_start: 0.7378 (mmm) cc_final: 0.7095 (tpt) REVERT: M 113 MET cc_start: 0.7317 (ppp) cc_final: 0.6994 (ppp) REVERT: N 32 GLN cc_start: 0.8383 (mp10) cc_final: 0.8169 (tp40) REVERT: N 188 ARG cc_start: 0.7848 (ptt-90) cc_final: 0.7622 (ptt90) REVERT: N 189 ARG cc_start: 0.7741 (ttm110) cc_final: 0.7374 (ttm170) REVERT: O 87 MET cc_start: 0.6122 (mpp) cc_final: 0.5813 (mpp) REVERT: O 118 MET cc_start: 0.5964 (mpp) cc_final: 0.5508 (mtt) REVERT: P 115 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8142 (tt0) REVERT: Q 17 GLU cc_start: 0.6984 (mp0) cc_final: 0.6181 (tm-30) REVERT: Q 87 THR cc_start: 0.8216 (p) cc_final: 0.7771 (p) REVERT: R 89 MET cc_start: 0.5982 (tpt) cc_final: 0.5650 (ptm) REVERT: R 97 ARG cc_start: 0.5889 (mtt-85) cc_final: 0.5399 (ttp80) REVERT: S 52 LYS cc_start: 0.8390 (mmtt) cc_final: 0.7924 (mmtt) REVERT: T 45 MET cc_start: 0.7018 (mtt) cc_final: 0.6661 (mtt) REVERT: T 159 MET cc_start: 0.6434 (pmm) cc_final: 0.4938 (mtp) REVERT: V 112 MET cc_start: 0.8339 (ttm) cc_final: 0.8043 (ttm) REVERT: X 68 ARG cc_start: 0.6188 (ppt170) cc_final: 0.5975 (ppt170) REVERT: X 148 ASP cc_start: 0.8929 (m-30) cc_final: 0.8642 (m-30) REVERT: X 152 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8940 (mttt) REVERT: Y 14 ASN cc_start: 0.8337 (m110) cc_final: 0.7626 (t0) REVERT: Y 17 ARG cc_start: 0.8417 (mtt90) cc_final: 0.7969 (mpt180) REVERT: Y 70 VAL cc_start: 0.7789 (t) cc_final: 0.7222 (m) REVERT: Y 132 LYS cc_start: 0.4978 (tmtt) cc_final: 0.4158 (mmtm) REVERT: Z 47 ASP cc_start: 0.7189 (t0) cc_final: 0.6879 (t70) REVERT: Z 73 LYS cc_start: 0.6440 (mmtt) cc_final: 0.6214 (mmtm) REVERT: Z 89 ILE cc_start: 0.4437 (tp) cc_final: 0.4205 (tt) REVERT: Z 92 ASP cc_start: 0.7530 (p0) cc_final: 0.7101 (p0) REVERT: Z 116 VAL cc_start: 0.8669 (t) cc_final: 0.8253 (p) REVERT: a 10 LYS cc_start: 0.7275 (mmtp) cc_final: 0.6855 (mmtp) REVERT: b 43 MET cc_start: 0.5375 (tpt) cc_final: 0.4989 (tpt) REVERT: b 57 MET cc_start: 0.2901 (ttm) cc_final: 0.2333 (tpt) REVERT: b 65 MET cc_start: 0.6843 (mmp) cc_final: 0.6144 (tmm) REVERT: d 44 ARG cc_start: 0.7197 (mmm-85) cc_final: 0.5945 (mmm-85) REVERT: d 67 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.7908 (mmp80) REVERT: d 96 GLU cc_start: 0.6753 (mp0) cc_final: 0.6497 (mp0) REVERT: e 69 MET cc_start: 0.7464 (ppp) cc_final: 0.7189 (ttp) REVERT: g 8 ARG cc_start: 0.7972 (ttm170) cc_final: 0.6289 (ttm-80) REVERT: g 18 ASN cc_start: 0.8566 (t0) cc_final: 0.8076 (t0) REVERT: g 32 TYR cc_start: 0.7915 (m-80) cc_final: 0.7714 (m-80) REVERT: g 100 GLN cc_start: 0.6597 (tm-30) cc_final: 0.6371 (tm-30) REVERT: h 52 LYS cc_start: 0.8131 (mptt) cc_final: 0.7721 (mptt) REVERT: i 58 MET cc_start: 0.4121 (mmm) cc_final: 0.3678 (ppp) REVERT: i 82 ARG cc_start: 0.4368 (mtt180) cc_final: 0.3761 (mtt180) REVERT: j 32 SER cc_start: 0.9547 (m) cc_final: 0.9212 (p) REVERT: j 50 SER cc_start: 0.9181 (p) cc_final: 0.8886 (p) REVERT: l 36 ARG cc_start: 0.8585 (mpp80) cc_final: 0.8319 (mtm-85) REVERT: n 14 LYS cc_start: 0.8389 (mtpt) cc_final: 0.7898 (mmtt) REVERT: p 31 ILE cc_start: 0.8389 (mm) cc_final: 0.8094 (tp) REVERT: s 192 VAL cc_start: 0.4951 (t) cc_final: 0.4668 (t) REVERT: x 34 TRP cc_start: 0.8639 (m100) cc_final: 0.8222 (m-10) REVERT: x 54 MET cc_start: 0.8494 (mmp) cc_final: 0.8127 (mmm) REVERT: x 160 LEU cc_start: 0.9208 (mt) cc_final: 0.8704 (mt) REVERT: x 163 LEU cc_start: 0.9311 (mt) cc_final: 0.8862 (mt) REVERT: x 166 ASP cc_start: 0.9225 (m-30) cc_final: 0.8937 (m-30) REVERT: x 167 GLU cc_start: 0.8838 (mt-10) cc_final: 0.7633 (tm-30) REVERT: x 171 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8556 (mmtt) REVERT: x 364 TYR cc_start: 0.8446 (t80) cc_final: 0.7929 (t80) REVERT: x 392 LYS cc_start: 0.9558 (mmtm) cc_final: 0.9285 (mptt) REVERT: x 406 GLU cc_start: 0.8430 (pp20) cc_final: 0.8048 (pp20) REVERT: x 431 LEU cc_start: 0.8908 (tp) cc_final: 0.8596 (tp) REVERT: y 38 MET cc_start: 0.7353 (ttp) cc_final: 0.6851 (mmt) REVERT: 1 451 PHE cc_start: 0.8215 (t80) cc_final: 0.7982 (t80) REVERT: 1 455 ILE cc_start: 0.9322 (mt) cc_final: 0.9022 (mt) REVERT: 1 458 ARG cc_start: 0.6375 (ttt180) cc_final: 0.5590 (mtt90) REVERT: 3 90 SER cc_start: 0.8837 (m) cc_final: 0.8117 (m) REVERT: 3 94 PHE cc_start: 0.9032 (m-10) cc_final: 0.8784 (m-80) REVERT: 3 136 ARG cc_start: 0.6958 (ttt-90) cc_final: 0.6606 (ttt180) REVERT: 4 12 ASN cc_start: 0.8978 (m-40) cc_final: 0.8672 (m110) REVERT: 5 1 MET cc_start: -0.0714 (ttp) cc_final: -0.2340 (mtm) REVERT: 5 35 LEU cc_start: 0.9601 (mt) cc_final: 0.9382 (mt) REVERT: 5 78 TYR cc_start: 0.8822 (t80) cc_final: 0.8299 (t80) REVERT: 5 114 ASN cc_start: 0.8780 (m110) cc_final: 0.7513 (m110) REVERT: 5 118 PHE cc_start: 0.8460 (m-10) cc_final: 0.7982 (m-10) REVERT: 5 192 ILE cc_start: 0.8690 (mm) cc_final: 0.8372 (mt) REVERT: 5 278 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8108 (tm-30) REVERT: 5 361 TYR cc_start: 0.8372 (t80) cc_final: 0.7980 (t80) REVERT: 5 431 LYS cc_start: 0.9235 (ptpp) cc_final: 0.8727 (pttt) REVERT: 5 461 ILE cc_start: 0.9302 (mt) cc_final: 0.8730 (mt) REVERT: 5 469 ILE cc_start: 0.9452 (pt) cc_final: 0.9138 (tp) REVERT: 5 483 TYR cc_start: 0.8733 (m-80) cc_final: 0.8382 (m-80) REVERT: 5 511 TRP cc_start: 0.7464 (t60) cc_final: 0.6542 (m100) REVERT: 5 568 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8608 (mm-30) outliers start: 7 outliers final: 1 residues processed: 1499 average time/residue: 1.4685 time to fit residues: 3775.7719 Evaluate side-chains 1188 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1186 time to evaluate : 7.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 1150 optimal weight: 0.9990 chunk 134 optimal weight: 0.2980 chunk 679 optimal weight: 30.0000 chunk 871 optimal weight: 40.0000 chunk 674 optimal weight: 10.0000 chunk 1004 optimal weight: 20.0000 chunk 666 optimal weight: 20.0000 chunk 1188 optimal weight: 5.9990 chunk 743 optimal weight: 40.0000 chunk 724 optimal weight: 20.0000 chunk 548 optimal weight: 0.9980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN B 276 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN D 244 HIS D 291 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN P 116 HIS R 34 ASN R 66 ASN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 163 HIS ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS T 139 HIS W 17 HIS X 111 GLN Y 20 ASN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 ASN ** m 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 HIS ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 34 ASN t 68 GLN ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 202 ASN x 300 ASN 5 101 HIS ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 551 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 165109 Z= 0.247 Angle : 0.755 19.985 242524 Z= 0.381 Chirality : 0.041 0.340 30251 Planarity : 0.006 0.134 15718 Dihedral : 25.469 179.746 73507 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.73 % Favored : 91.66 % Rotamer: Outliers : 0.09 % Allowed : 2.17 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.09), residues: 8227 helix: 0.01 (0.09), residues: 3265 sheet: -1.31 (0.16), residues: 925 loop : -1.93 (0.09), residues: 4037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP I 171 HIS 0.022 0.002 HIS x 404 PHE 0.045 0.002 PHE x 182 TYR 0.037 0.002 TYR 5 392 ARG 0.016 0.001 ARG f 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1512 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1506 time to evaluate : 9.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.6470 (mm-30) cc_final: 0.6266 (mm-30) REVERT: A 241 ARG cc_start: 0.7760 (mpt180) cc_final: 0.7271 (mpt180) REVERT: B 211 PHE cc_start: 0.4438 (m-80) cc_final: 0.4105 (m-10) REVERT: C 65 GLU cc_start: 0.9128 (tp30) cc_final: 0.8733 (pt0) REVERT: C 101 MET cc_start: 0.5763 (ptm) cc_final: 0.4633 (tpt) REVERT: C 106 LYS cc_start: 0.6815 (pttm) cc_final: 0.6407 (pttt) REVERT: C 161 TYR cc_start: 0.6264 (m-80) cc_final: 0.5520 (m-80) REVERT: C 320 LYS cc_start: 0.4951 (tptt) cc_final: 0.4627 (mmmt) REVERT: D 242 LYS cc_start: 0.9093 (pttm) cc_final: 0.8816 (mmtm) REVERT: D 275 GLN cc_start: 0.7317 (mt0) cc_final: 0.6589 (mm-40) REVERT: D 287 PHE cc_start: 0.7752 (m-80) cc_final: 0.7443 (m-80) REVERT: H 128 MET cc_start: 0.4878 (mmt) cc_final: 0.4652 (mmt) REVERT: H 143 GLU cc_start: 0.5458 (tp30) cc_final: 0.5017 (tp30) REVERT: I 21 ARG cc_start: 0.8017 (ptm-80) cc_final: 0.7813 (ptt180) REVERT: I 208 LYS cc_start: 0.7187 (pttm) cc_final: 0.6984 (pttt) REVERT: L 8 MET cc_start: 0.7228 (mtt) cc_final: 0.5904 (ttp) REVERT: L 173 GLU cc_start: 0.7770 (pt0) cc_final: 0.7271 (tp30) REVERT: L 184 MET cc_start: 0.7341 (mmm) cc_final: 0.6921 (tpt) REVERT: N 189 ARG cc_start: 0.7559 (ttm110) cc_final: 0.7291 (ttm170) REVERT: O 87 MET cc_start: 0.5934 (mpp) cc_final: 0.5614 (mpp) REVERT: O 118 MET cc_start: 0.5611 (mpp) cc_final: 0.5054 (mtt) REVERT: Q 87 THR cc_start: 0.8294 (p) cc_final: 0.7921 (p) REVERT: R 89 MET cc_start: 0.5958 (tpt) cc_final: 0.5717 (ptm) REVERT: S 52 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7706 (mmtt) REVERT: S 113 MET cc_start: 0.3928 (mmp) cc_final: 0.3681 (mmm) REVERT: T 31 MET cc_start: 0.6406 (mpp) cc_final: 0.5360 (mpp) REVERT: T 45 MET cc_start: 0.6845 (mtt) cc_final: 0.6553 (mtt) REVERT: T 159 MET cc_start: 0.6542 (pmm) cc_final: 0.5011 (mtp) REVERT: U 34 MET cc_start: 0.6712 (ppp) cc_final: 0.5831 (ppp) REVERT: U 73 THR cc_start: 0.7376 (m) cc_final: 0.7083 (p) REVERT: V 112 MET cc_start: 0.8272 (ttm) cc_final: 0.7987 (ttm) REVERT: X 68 ARG cc_start: 0.6073 (ppt170) cc_final: 0.5121 (tmm160) REVERT: X 116 LEU cc_start: 0.8766 (tp) cc_final: 0.8290 (tp) REVERT: X 148 ASP cc_start: 0.8912 (m-30) cc_final: 0.8591 (m-30) REVERT: Y 14 ASN cc_start: 0.8064 (m110) cc_final: 0.7438 (t0) REVERT: Y 17 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8153 (mpt180) REVERT: Y 70 VAL cc_start: 0.7664 (t) cc_final: 0.7126 (m) REVERT: Y 132 LYS cc_start: 0.3676 (tmtt) cc_final: 0.3047 (mmtm) REVERT: Z 47 ASP cc_start: 0.7173 (t0) cc_final: 0.6887 (t70) REVERT: Z 73 LYS cc_start: 0.6476 (mmtt) cc_final: 0.6203 (mmtm) REVERT: Z 89 ILE cc_start: 0.4422 (tp) cc_final: 0.4210 (tt) REVERT: Z 92 ASP cc_start: 0.7473 (p0) cc_final: 0.7172 (p0) REVERT: Z 111 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.8007 (mmt-90) REVERT: Z 116 VAL cc_start: 0.8655 (t) cc_final: 0.8240 (p) REVERT: a 10 LYS cc_start: 0.7287 (mmtp) cc_final: 0.6894 (mmtp) REVERT: a 58 MET cc_start: 0.5008 (mpp) cc_final: 0.4740 (mpp) REVERT: b 57 MET cc_start: 0.2378 (ttm) cc_final: 0.2008 (tpt) REVERT: b 65 MET cc_start: 0.6848 (mmp) cc_final: 0.6141 (tmm) REVERT: c 21 VAL cc_start: 0.7941 (t) cc_final: 0.7739 (t) REVERT: d 67 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.7965 (mmp80) REVERT: e 27 ARG cc_start: 0.6844 (mmm160) cc_final: 0.6558 (mmt-90) REVERT: e 69 MET cc_start: 0.7387 (ppp) cc_final: 0.7019 (ttp) REVERT: e 88 LEU cc_start: 0.5887 (tp) cc_final: 0.5626 (tt) REVERT: e 98 GLU cc_start: 0.6663 (mp0) cc_final: 0.6283 (mp0) REVERT: g 8 ARG cc_start: 0.8052 (ttm170) cc_final: 0.6581 (ttm-80) REVERT: g 18 ASN cc_start: 0.8467 (t0) cc_final: 0.8008 (t0) REVERT: g 32 TYR cc_start: 0.8115 (m-80) cc_final: 0.7825 (m-80) REVERT: g 100 GLN cc_start: 0.6629 (tm-30) cc_final: 0.6385 (tm-30) REVERT: g 104 VAL cc_start: 0.7562 (t) cc_final: 0.7360 (t) REVERT: h 25 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7371 (mtpt) REVERT: h 52 LYS cc_start: 0.8180 (mptt) cc_final: 0.7802 (mptt) REVERT: i 58 MET cc_start: 0.4116 (mmm) cc_final: 0.3725 (ppp) REVERT: i 82 ARG cc_start: 0.4293 (mtt180) cc_final: 0.3721 (mtt180) REVERT: j 32 SER cc_start: 0.9479 (m) cc_final: 0.9077 (p) REVERT: j 50 SER cc_start: 0.9204 (p) cc_final: 0.8986 (p) REVERT: j 78 PHE cc_start: 0.7090 (m-10) cc_final: 0.6878 (m-10) REVERT: k 3 ARG cc_start: 0.5859 (mmp80) cc_final: 0.5475 (mmp80) REVERT: l 36 ARG cc_start: 0.8528 (mpp80) cc_final: 0.8226 (mtt180) REVERT: n 2 ARG cc_start: 0.6365 (ttt180) cc_final: 0.5132 (mtm180) REVERT: n 14 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7884 (mmtt) REVERT: p 31 ILE cc_start: 0.8381 (mm) cc_final: 0.8118 (tp) REVERT: r 97 ILE cc_start: 0.7303 (pt) cc_final: 0.7086 (tp) REVERT: s 101 MET cc_start: 0.1334 (ppp) cc_final: 0.0901 (ptp) REVERT: s 192 VAL cc_start: 0.5455 (t) cc_final: 0.5208 (t) REVERT: x 54 MET cc_start: 0.8481 (mmp) cc_final: 0.8070 (mmm) REVERT: x 160 LEU cc_start: 0.9272 (mt) cc_final: 0.8777 (mt) REVERT: x 163 LEU cc_start: 0.9327 (mt) cc_final: 0.8934 (mt) REVERT: x 166 ASP cc_start: 0.9212 (m-30) cc_final: 0.9011 (m-30) REVERT: x 167 GLU cc_start: 0.8774 (mt-10) cc_final: 0.7504 (tm-30) REVERT: x 168 LEU cc_start: 0.8922 (mt) cc_final: 0.8672 (mt) REVERT: x 171 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8524 (mmtt) REVERT: x 392 LYS cc_start: 0.9519 (mmtm) cc_final: 0.9168 (mmtm) REVERT: x 406 GLU cc_start: 0.8395 (pp20) cc_final: 0.8186 (pp20) REVERT: x 415 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7809 (ptp90) REVERT: y 38 MET cc_start: 0.6816 (ttp) cc_final: 0.6453 (mmt) REVERT: y 52 PHE cc_start: 0.6825 (m-10) cc_final: 0.6359 (m-10) REVERT: 1 451 PHE cc_start: 0.8194 (t80) cc_final: 0.7957 (t80) REVERT: 1 455 ILE cc_start: 0.9296 (mt) cc_final: 0.9000 (mt) REVERT: 1 458 ARG cc_start: 0.6271 (ttt180) cc_final: 0.5622 (tpp80) REVERT: 3 90 SER cc_start: 0.9031 (m) cc_final: 0.8149 (p) REVERT: 3 94 PHE cc_start: 0.8920 (m-10) cc_final: 0.8672 (m-80) REVERT: 4 12 ASN cc_start: 0.8965 (m-40) cc_final: 0.8607 (m-40) REVERT: 5 1 MET cc_start: -0.0779 (ttp) cc_final: -0.2447 (mtm) REVERT: 5 78 TYR cc_start: 0.8741 (t80) cc_final: 0.8218 (t80) REVERT: 5 114 ASN cc_start: 0.8794 (m110) cc_final: 0.7267 (m-40) REVERT: 5 118 PHE cc_start: 0.8436 (m-10) cc_final: 0.7680 (m-10) REVERT: 5 166 TYR cc_start: 0.7270 (t80) cc_final: 0.6746 (t80) REVERT: 5 278 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8047 (tm-30) REVERT: 5 357 TRP cc_start: 0.9107 (p-90) cc_final: 0.8896 (p-90) REVERT: 5 361 TYR cc_start: 0.8383 (t80) cc_final: 0.8075 (t80) REVERT: 5 370 MET cc_start: 0.8579 (tpp) cc_final: 0.7568 (tpp) REVERT: 5 398 TYR cc_start: 0.8851 (t80) cc_final: 0.8356 (t80) REVERT: 5 418 SER cc_start: 0.9466 (m) cc_final: 0.8749 (p) REVERT: 5 469 ILE cc_start: 0.9479 (pt) cc_final: 0.9178 (tp) REVERT: 5 483 TYR cc_start: 0.8731 (m-80) cc_final: 0.8380 (m-80) REVERT: 5 511 TRP cc_start: 0.7396 (t60) cc_final: 0.6541 (m100) REVERT: 5 559 MET cc_start: 0.8585 (ptm) cc_final: 0.8256 (ppp) REVERT: 5 568 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8595 (mm-30) REVERT: 5 599 MET cc_start: 0.8948 (mpp) cc_final: 0.8382 (mpp) REVERT: 5 639 MET cc_start: 0.8601 (mpp) cc_final: 0.7492 (mpp) REVERT: 5 640 TYR cc_start: 0.5477 (t80) cc_final: 0.5087 (t80) REVERT: 5 643 CYS cc_start: 0.8603 (m) cc_final: 0.7873 (t) REVERT: 5 664 ARG cc_start: 0.7601 (mpp-170) cc_final: 0.7367 (mtm-85) REVERT: 5 671 LYS cc_start: 0.8424 (tmtt) cc_final: 0.8181 (tptt) outliers start: 6 outliers final: 3 residues processed: 1508 average time/residue: 1.3887 time to fit residues: 3589.3505 Evaluate side-chains 1203 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1200 time to evaluate : 7.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 735 optimal weight: 30.0000 chunk 474 optimal weight: 9.9990 chunk 709 optimal weight: 10.0000 chunk 357 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 755 optimal weight: 30.0000 chunk 809 optimal weight: 20.0000 chunk 587 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 934 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS B 123 HIS ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS B 276 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS D 291 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN G 64 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN ** I 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 17 GLN U 50 ASN W 17 HIS ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS a 34 ASN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 34 ASN f 80 ASN h 20 GLN l 19 GLN ** m 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 ASN ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 202 ASN ** x 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 397 GLN ** x 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 165109 Z= 0.374 Angle : 0.889 22.791 242524 Z= 0.445 Chirality : 0.046 0.351 30251 Planarity : 0.007 0.137 15718 Dihedral : 25.613 179.668 73507 Min Nonbonded Distance : 1.067 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.76 % Favored : 89.69 % Rotamer: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.09), residues: 8227 helix: -0.33 (0.09), residues: 3242 sheet: -1.50 (0.16), residues: 908 loop : -2.13 (0.09), residues: 4077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP L 18 HIS 0.026 0.002 HIS 5 267 PHE 0.058 0.003 PHE I 119 TYR 0.048 0.003 TYR 5 100 ARG 0.021 0.001 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1432 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1428 time to evaluate : 7.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6295 (mm-30) REVERT: A 241 ARG cc_start: 0.7797 (mpt180) cc_final: 0.7470 (mpt180) REVERT: B 169 ARG cc_start: 0.7409 (tpm170) cc_final: 0.7189 (tpm170) REVERT: B 211 PHE cc_start: 0.3793 (m-80) cc_final: 0.3552 (m-80) REVERT: C 65 GLU cc_start: 0.9102 (tp30) cc_final: 0.8798 (pt0) REVERT: C 101 MET cc_start: 0.6090 (ptm) cc_final: 0.5687 (ptm) REVERT: C 161 TYR cc_start: 0.6747 (m-80) cc_final: 0.5968 (m-80) REVERT: C 284 MET cc_start: 0.6176 (ptm) cc_final: 0.5354 (tmm) REVERT: D 242 LYS cc_start: 0.9122 (pttm) cc_final: 0.8868 (mmtm) REVERT: D 275 GLN cc_start: 0.7048 (mt0) cc_final: 0.6377 (mm-40) REVERT: D 287 PHE cc_start: 0.7770 (m-80) cc_final: 0.7460 (m-80) REVERT: E 187 GLN cc_start: 0.5931 (OUTLIER) cc_final: 0.5338 (pp30) REVERT: E 257 ILE cc_start: 0.8049 (pt) cc_final: 0.7510 (mt) REVERT: F 134 MET cc_start: 0.6373 (mmt) cc_final: 0.5532 (mmp) REVERT: I 56 GLU cc_start: 0.5161 (tp30) cc_final: 0.4922 (mm-30) REVERT: I 153 ARG cc_start: 0.8147 (tmm-80) cc_final: 0.7813 (tmm-80) REVERT: J 175 LEU cc_start: 0.7871 (tp) cc_final: 0.7583 (tp) REVERT: L 8 MET cc_start: 0.7072 (mtt) cc_final: 0.6108 (ttm) REVERT: L 173 GLU cc_start: 0.7921 (pt0) cc_final: 0.7354 (tp30) REVERT: L 184 MET cc_start: 0.7426 (mmm) cc_final: 0.7062 (tpt) REVERT: N 32 GLN cc_start: 0.8486 (mp10) cc_final: 0.8196 (tp40) REVERT: N 161 MET cc_start: 0.8110 (mmt) cc_final: 0.7337 (mpp) REVERT: N 189 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7411 (ttm170) REVERT: O 87 MET cc_start: 0.6445 (mpp) cc_final: 0.6045 (mpp) REVERT: O 118 MET cc_start: 0.5764 (mpp) cc_final: 0.5339 (mtt) REVERT: Q 87 THR cc_start: 0.8233 (p) cc_final: 0.7766 (p) REVERT: R 27 ASN cc_start: 0.8328 (m-40) cc_final: 0.8097 (m-40) REVERT: S 27 LEU cc_start: 0.8044 (tt) cc_final: 0.7837 (tt) REVERT: S 52 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7770 (mmtt) REVERT: T 159 MET cc_start: 0.6417 (pmm) cc_final: 0.4719 (mtt) REVERT: U 73 THR cc_start: 0.7387 (m) cc_final: 0.7113 (p) REVERT: V 112 MET cc_start: 0.8353 (ttm) cc_final: 0.8102 (ttm) REVERT: X 68 ARG cc_start: 0.6219 (ppt170) cc_final: 0.5924 (tmm160) REVERT: X 148 ASP cc_start: 0.9049 (m-30) cc_final: 0.8807 (m-30) REVERT: X 152 LYS cc_start: 0.9249 (mtmm) cc_final: 0.8988 (mttt) REVERT: Y 3 PHE cc_start: 0.6596 (m-80) cc_final: 0.6384 (m-10) REVERT: Y 14 ASN cc_start: 0.8258 (m110) cc_final: 0.7312 (t0) REVERT: Y 70 VAL cc_start: 0.7919 (t) cc_final: 0.7384 (m) REVERT: Y 132 LYS cc_start: 0.3991 (tmtt) cc_final: 0.3340 (mmtm) REVERT: Z 29 ILE cc_start: 0.8215 (tt) cc_final: 0.7538 (mm) REVERT: Z 47 ASP cc_start: 0.7599 (t0) cc_final: 0.7204 (t70) REVERT: Z 57 MET cc_start: 0.7351 (ppp) cc_final: 0.7082 (ppp) REVERT: Z 62 ILE cc_start: 0.7203 (mt) cc_final: 0.6945 (mt) REVERT: Z 73 LYS cc_start: 0.6667 (mmtt) cc_final: 0.6378 (mmtm) REVERT: Z 116 VAL cc_start: 0.8739 (t) cc_final: 0.8358 (p) REVERT: a 10 LYS cc_start: 0.7478 (mmtp) cc_final: 0.7020 (mmtp) REVERT: a 84 GLU cc_start: 0.4846 (pp20) cc_final: 0.3193 (mm-30) REVERT: b 57 MET cc_start: 0.2542 (ttm) cc_final: 0.2316 (tpt) REVERT: b 65 MET cc_start: 0.7213 (mmp) cc_final: 0.6476 (tmm) REVERT: c 21 VAL cc_start: 0.7967 (t) cc_final: 0.7726 (t) REVERT: d 67 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.7912 (mmp80) REVERT: e 69 MET cc_start: 0.7715 (ppp) cc_final: 0.7330 (ptt) REVERT: e 88 LEU cc_start: 0.6176 (tp) cc_final: 0.5969 (tt) REVERT: g 8 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7377 (ttm-80) REVERT: g 18 ASN cc_start: 0.8549 (t0) cc_final: 0.8056 (t0) REVERT: g 100 GLN cc_start: 0.6576 (tm-30) cc_final: 0.6357 (tm-30) REVERT: g 104 VAL cc_start: 0.7627 (t) cc_final: 0.7398 (t) REVERT: h 25 LYS cc_start: 0.7665 (mtmt) cc_final: 0.7399 (mmmt) REVERT: h 44 LEU cc_start: 0.8597 (mt) cc_final: 0.8393 (mt) REVERT: h 52 LYS cc_start: 0.8229 (mptt) cc_final: 0.7706 (tptt) REVERT: i 58 MET cc_start: 0.4309 (mmm) cc_final: 0.3827 (ppp) REVERT: i 82 ARG cc_start: 0.3788 (mtt180) cc_final: 0.3327 (mtt180) REVERT: j 32 SER cc_start: 0.9557 (m) cc_final: 0.9193 (p) REVERT: j 50 SER cc_start: 0.9245 (p) cc_final: 0.8973 (p) REVERT: j 78 PHE cc_start: 0.6976 (m-10) cc_final: 0.6687 (m-80) REVERT: k 68 GLU cc_start: 0.7239 (tm-30) cc_final: 0.7010 (tm-30) REVERT: n 14 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7945 (mmtt) REVERT: o 28 LYS cc_start: 0.5700 (mmpt) cc_final: 0.4634 (mmmt) REVERT: r 125 MET cc_start: 0.2505 (pmm) cc_final: 0.0995 (mmm) REVERT: s 101 MET cc_start: 0.1251 (ppp) cc_final: 0.0907 (ptp) REVERT: x 54 MET cc_start: 0.8509 (mmp) cc_final: 0.7933 (mmm) REVERT: x 160 LEU cc_start: 0.9300 (mt) cc_final: 0.8830 (mt) REVERT: x 167 GLU cc_start: 0.8797 (mt-10) cc_final: 0.7761 (tm-30) REVERT: x 168 LEU cc_start: 0.9063 (mt) cc_final: 0.8821 (mt) REVERT: x 171 LYS cc_start: 0.8911 (mtmt) cc_final: 0.8563 (mmtt) REVERT: x 364 TYR cc_start: 0.8453 (t80) cc_final: 0.8067 (t80) REVERT: x 392 LYS cc_start: 0.9590 (mmtm) cc_final: 0.9134 (mmtm) REVERT: x 406 GLU cc_start: 0.8583 (pp20) cc_final: 0.8314 (pp20) REVERT: x 415 ARG cc_start: 0.8518 (ptp90) cc_final: 0.8003 (ptp90) REVERT: y 38 MET cc_start: 0.6848 (ttt) cc_final: 0.6423 (mmt) REVERT: z 76 MET cc_start: 0.8349 (ptp) cc_final: 0.7580 (tpt) REVERT: z 79 LEU cc_start: 0.8418 (tt) cc_final: 0.8159 (tt) REVERT: 1 451 PHE cc_start: 0.8374 (t80) cc_final: 0.8063 (t80) REVERT: 1 455 ILE cc_start: 0.9332 (mt) cc_final: 0.9039 (mt) REVERT: 1 458 ARG cc_start: 0.6237 (ttt180) cc_final: 0.5518 (mtt90) REVERT: 3 90 SER cc_start: 0.9019 (m) cc_final: 0.8367 (m) REVERT: 3 94 PHE cc_start: 0.8978 (m-10) cc_final: 0.8755 (m-80) REVERT: 4 12 ASN cc_start: 0.8941 (m-40) cc_final: 0.8639 (m-40) REVERT: 5 1 MET cc_start: -0.0396 (ttp) cc_final: -0.2065 (mtm) REVERT: 5 78 TYR cc_start: 0.8826 (t80) cc_final: 0.8275 (t80) REVERT: 5 114 ASN cc_start: 0.8855 (m110) cc_final: 0.7868 (m110) REVERT: 5 118 PHE cc_start: 0.8390 (m-10) cc_final: 0.7993 (m-10) REVERT: 5 182 MET cc_start: 0.8343 (mmp) cc_final: 0.7757 (mmp) REVERT: 5 198 CYS cc_start: 0.7572 (m) cc_final: 0.7077 (m) REVERT: 5 268 MET cc_start: 0.7555 (mtt) cc_final: 0.6827 (mtt) REVERT: 5 357 TRP cc_start: 0.9187 (p-90) cc_final: 0.8754 (p-90) REVERT: 5 361 TYR cc_start: 0.8307 (t80) cc_final: 0.8090 (t80) REVERT: 5 378 CYS cc_start: 0.9322 (m) cc_final: 0.9039 (m) REVERT: 5 398 TYR cc_start: 0.9010 (t80) cc_final: 0.8548 (t80) REVERT: 5 461 ILE cc_start: 0.9354 (mt) cc_final: 0.8862 (mt) REVERT: 5 469 ILE cc_start: 0.9499 (pt) cc_final: 0.9222 (tp) REVERT: 5 483 TYR cc_start: 0.8750 (m-80) cc_final: 0.8413 (m-80) REVERT: 5 511 TRP cc_start: 0.7478 (t60) cc_final: 0.6498 (t-100) REVERT: 5 523 MET cc_start: 0.7605 (mtp) cc_final: 0.7367 (mmm) REVERT: 5 559 MET cc_start: 0.8758 (ptm) cc_final: 0.8282 (ppp) REVERT: 5 568 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8578 (mm-30) REVERT: 5 599 MET cc_start: 0.8880 (mpp) cc_final: 0.8335 (mpp) REVERT: 5 643 CYS cc_start: 0.8784 (m) cc_final: 0.8191 (t) REVERT: 5 664 ARG cc_start: 0.7638 (mpp-170) cc_final: 0.7377 (mtm-85) outliers start: 4 outliers final: 1 residues processed: 1431 average time/residue: 1.3851 time to fit residues: 3408.3443 Evaluate side-chains 1159 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1157 time to evaluate : 7.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 1081 optimal weight: 3.9990 chunk 1138 optimal weight: 0.8980 chunk 1038 optimal weight: 30.0000 chunk 1107 optimal weight: 0.9980 chunk 666 optimal weight: 20.0000 chunk 482 optimal weight: 0.0060 chunk 869 optimal weight: 20.0000 chunk 339 optimal weight: 5.9990 chunk 1000 optimal weight: 10.0000 chunk 1047 optimal weight: 10.0000 chunk 1103 optimal weight: 2.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS C 343 GLN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN H 156 ASN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 ASN ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN Q 45 GLN Q 57 ASN R 121 HIS R 130 ASN S 156 HIS ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 GLN Y 20 ASN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN e 34 ASN f 99 HIS ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 HIS ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 397 GLN x 465 GLN 5 352 HIS ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 545 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 165109 Z= 0.192 Angle : 0.722 20.812 242524 Z= 0.363 Chirality : 0.039 0.309 30251 Planarity : 0.006 0.134 15718 Dihedral : 25.453 179.925 73507 Min Nonbonded Distance : 1.170 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.37 % Favored : 92.10 % Rotamer: Outliers : 0.07 % Allowed : 0.88 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.09), residues: 8227 helix: 0.05 (0.09), residues: 3236 sheet: -1.34 (0.16), residues: 914 loop : -1.91 (0.09), residues: 4077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 196 HIS 0.023 0.001 HIS 5 222 PHE 0.058 0.002 PHE x 196 TYR 0.037 0.002 TYR 5 392 ARG 0.012 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1465 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1460 time to evaluate : 7.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6312 (mm-30) REVERT: A 207 VAL cc_start: 0.9402 (m) cc_final: 0.9196 (p) REVERT: A 241 ARG cc_start: 0.7640 (mpt180) cc_final: 0.6926 (mpt180) REVERT: B 90 VAL cc_start: 0.7186 (p) cc_final: 0.6534 (p) REVERT: B 211 PHE cc_start: 0.4060 (m-80) cc_final: 0.3850 (m-80) REVERT: C 65 GLU cc_start: 0.9046 (tp30) cc_final: 0.8693 (pt0) REVERT: C 101 MET cc_start: 0.5779 (ptm) cc_final: 0.5388 (ptm) REVERT: C 122 TYR cc_start: 0.7084 (t80) cc_final: 0.6405 (t80) REVERT: C 161 TYR cc_start: 0.6301 (m-80) cc_final: 0.5837 (m-80) REVERT: C 341 LEU cc_start: 0.7606 (pp) cc_final: 0.6304 (tp) REVERT: D 51 MET cc_start: 0.5646 (ppp) cc_final: 0.5386 (ppp) REVERT: D 113 PHE cc_start: 0.7237 (m-80) cc_final: 0.6987 (m-80) REVERT: D 242 LYS cc_start: 0.9079 (pttm) cc_final: 0.8783 (mmtm) REVERT: D 275 GLN cc_start: 0.6826 (mt0) cc_final: 0.6179 (mm-40) REVERT: D 287 PHE cc_start: 0.7913 (m-80) cc_final: 0.7557 (m-80) REVERT: E 257 ILE cc_start: 0.7969 (pt) cc_final: 0.7479 (mt) REVERT: H 60 TRP cc_start: 0.4850 (m-90) cc_final: 0.4222 (m-90) REVERT: H 143 GLU cc_start: 0.5489 (tp30) cc_final: 0.5132 (tp30) REVERT: I 56 GLU cc_start: 0.4678 (tp30) cc_final: 0.4413 (mm-30) REVERT: I 153 ARG cc_start: 0.8215 (tmm-80) cc_final: 0.7923 (tmm-80) REVERT: J 175 LEU cc_start: 0.7975 (tp) cc_final: 0.7758 (tp) REVERT: L 8 MET cc_start: 0.7156 (mtt) cc_final: 0.5909 (ttp) REVERT: L 173 GLU cc_start: 0.7773 (pt0) cc_final: 0.7290 (tp30) REVERT: L 184 MET cc_start: 0.7307 (mmm) cc_final: 0.6872 (tpt) REVERT: N 189 ARG cc_start: 0.7313 (ttm110) cc_final: 0.7033 (ttm170) REVERT: O 87 MET cc_start: 0.6111 (mpp) cc_final: 0.5793 (mpp) REVERT: O 118 MET cc_start: 0.5706 (mpp) cc_final: 0.5404 (mtt) REVERT: Q 87 THR cc_start: 0.8376 (p) cc_final: 0.8119 (p) REVERT: R 27 ASN cc_start: 0.8305 (m-40) cc_final: 0.8089 (m-40) REVERT: R 34 ASN cc_start: 0.7405 (t0) cc_final: 0.6672 (m-40) REVERT: S 52 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7614 (mmtt) REVERT: T 31 MET cc_start: 0.6255 (mpp) cc_final: 0.5210 (mpp) REVERT: T 159 MET cc_start: 0.6652 (pmm) cc_final: 0.4935 (mtt) REVERT: U 34 MET cc_start: 0.6573 (ppp) cc_final: 0.5862 (ppp) REVERT: U 73 THR cc_start: 0.7084 (m) cc_final: 0.6787 (p) REVERT: V 112 MET cc_start: 0.8255 (ttm) cc_final: 0.8017 (ttm) REVERT: X 68 ARG cc_start: 0.6172 (ppt170) cc_final: 0.5397 (tmm160) REVERT: X 116 LEU cc_start: 0.8506 (mm) cc_final: 0.7510 (tp) REVERT: Y 17 ARG cc_start: 0.8406 (mpt180) cc_final: 0.8148 (mpt180) REVERT: Y 62 TYR cc_start: 0.7307 (m-80) cc_final: 0.7006 (m-10) REVERT: Y 70 VAL cc_start: 0.7493 (t) cc_final: 0.6921 (m) REVERT: Y 132 LYS cc_start: 0.3611 (tmtt) cc_final: 0.3396 (tttt) REVERT: Z 47 ASP cc_start: 0.7405 (t0) cc_final: 0.7089 (t70) REVERT: Z 73 LYS cc_start: 0.6397 (mmtt) cc_final: 0.6108 (mmtm) REVERT: Z 116 VAL cc_start: 0.8684 (t) cc_final: 0.8316 (p) REVERT: a 10 LYS cc_start: 0.7076 (mmtp) cc_final: 0.6825 (mmtp) REVERT: b 43 MET cc_start: 0.5679 (tpt) cc_final: 0.5095 (tpp) REVERT: b 57 MET cc_start: 0.2378 (ttm) cc_final: 0.2005 (tpt) REVERT: b 65 MET cc_start: 0.7176 (mmp) cc_final: 0.6443 (tmm) REVERT: c 21 VAL cc_start: 0.7992 (t) cc_final: 0.7760 (t) REVERT: d 67 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7742 (mmp80) REVERT: e 69 MET cc_start: 0.7498 (ppp) cc_final: 0.6968 (ttp) REVERT: e 88 LEU cc_start: 0.6265 (tp) cc_final: 0.6057 (tt) REVERT: e 98 GLU cc_start: 0.6604 (mp0) cc_final: 0.5991 (mp0) REVERT: g 5 LEU cc_start: 0.8672 (pt) cc_final: 0.8187 (pt) REVERT: g 18 ASN cc_start: 0.8339 (t0) cc_final: 0.7980 (t0) REVERT: g 104 VAL cc_start: 0.7681 (t) cc_final: 0.7449 (t) REVERT: h 22 ASP cc_start: 0.5823 (t0) cc_final: 0.5592 (t0) REVERT: h 25 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7396 (mtpt) REVERT: h 52 LYS cc_start: 0.8162 (mptt) cc_final: 0.7537 (tptt) REVERT: i 82 ARG cc_start: 0.3923 (mtt180) cc_final: 0.3567 (mtt180) REVERT: i 97 MET cc_start: 0.2499 (ptm) cc_final: 0.2129 (ptp) REVERT: j 32 SER cc_start: 0.9422 (m) cc_final: 0.9005 (p) REVERT: j 50 SER cc_start: 0.9229 (p) cc_final: 0.8981 (p) REVERT: n 14 LYS cc_start: 0.8407 (mtpt) cc_final: 0.7932 (mmtt) REVERT: o 28 LYS cc_start: 0.5332 (mmpt) cc_final: 0.4396 (mmmt) REVERT: p 31 ILE cc_start: 0.8525 (mm) cc_final: 0.8199 (tp) REVERT: s 60 MET cc_start: 0.1310 (mtp) cc_final: 0.0983 (mmm) REVERT: s 95 LEU cc_start: -0.0961 (pp) cc_final: -0.1356 (pt) REVERT: t 10 ILE cc_start: 0.1299 (mm) cc_final: 0.1065 (tp) REVERT: x 54 MET cc_start: 0.8435 (mmp) cc_final: 0.7711 (mmp) REVERT: x 91 MET cc_start: 0.8239 (ttm) cc_final: 0.8026 (ttm) REVERT: x 112 PHE cc_start: 0.8908 (t80) cc_final: 0.8603 (t80) REVERT: x 160 LEU cc_start: 0.9343 (mt) cc_final: 0.9067 (mt) REVERT: x 163 LEU cc_start: 0.9320 (mt) cc_final: 0.8864 (mt) REVERT: x 167 GLU cc_start: 0.8795 (mt-10) cc_final: 0.7557 (tm-30) REVERT: x 168 LEU cc_start: 0.8935 (mt) cc_final: 0.8727 (mt) REVERT: x 171 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8555 (mtpp) REVERT: x 392 LYS cc_start: 0.9541 (mmtm) cc_final: 0.9063 (mmtm) REVERT: x 415 ARG cc_start: 0.8007 (ptp90) cc_final: 0.7752 (ptp90) REVERT: y 35 LYS cc_start: 0.8541 (tptp) cc_final: 0.8328 (tptp) REVERT: y 38 MET cc_start: 0.6534 (ttt) cc_final: 0.6314 (mmt) REVERT: y 44 PHE cc_start: 0.9148 (t80) cc_final: 0.8854 (t80) REVERT: z 76 MET cc_start: 0.8273 (ptp) cc_final: 0.7547 (tpt) REVERT: z 79 LEU cc_start: 0.8419 (tt) cc_final: 0.8156 (tt) REVERT: 1 451 PHE cc_start: 0.8322 (t80) cc_final: 0.7985 (t80) REVERT: 1 455 ILE cc_start: 0.9294 (mt) cc_final: 0.9017 (mt) REVERT: 1 458 ARG cc_start: 0.6293 (ttt180) cc_final: 0.5568 (mtt90) REVERT: 3 90 SER cc_start: 0.8993 (m) cc_final: 0.8438 (p) REVERT: 4 10 PHE cc_start: 0.6552 (m-80) cc_final: 0.6305 (m-80) REVERT: 4 12 ASN cc_start: 0.8935 (m-40) cc_final: 0.8607 (m-40) REVERT: 5 1 MET cc_start: -0.0529 (ttp) cc_final: -0.2317 (mtm) REVERT: 5 78 TYR cc_start: 0.8866 (t80) cc_final: 0.8222 (t80) REVERT: 5 114 ASN cc_start: 0.8740 (m110) cc_final: 0.7407 (m-40) REVERT: 5 118 PHE cc_start: 0.8410 (m-10) cc_final: 0.7669 (m-10) REVERT: 5 182 MET cc_start: 0.8682 (mmp) cc_final: 0.8124 (mmt) REVERT: 5 198 CYS cc_start: 0.7200 (m) cc_final: 0.6918 (m) REVERT: 5 357 TRP cc_start: 0.9033 (p-90) cc_final: 0.8769 (p-90) REVERT: 5 370 MET cc_start: 0.8462 (tpp) cc_final: 0.7531 (tpp) REVERT: 5 389 ILE cc_start: 0.9678 (mp) cc_final: 0.9473 (mp) REVERT: 5 403 MET cc_start: 0.8252 (mmp) cc_final: 0.8014 (mmm) REVERT: 5 410 LEU cc_start: 0.9318 (mt) cc_final: 0.9005 (mt) REVERT: 5 418 SER cc_start: 0.9394 (m) cc_final: 0.8769 (p) REVERT: 5 461 ILE cc_start: 0.9125 (mt) cc_final: 0.8742 (mt) REVERT: 5 469 ILE cc_start: 0.9493 (pt) cc_final: 0.9245 (tp) REVERT: 5 483 TYR cc_start: 0.8798 (m-80) cc_final: 0.8349 (m-80) REVERT: 5 511 TRP cc_start: 0.7202 (t60) cc_final: 0.6435 (m100) REVERT: 5 523 MET cc_start: 0.7636 (mtp) cc_final: 0.7435 (mmm) REVERT: 5 559 MET cc_start: 0.8700 (ptm) cc_final: 0.8377 (ppp) REVERT: 5 568 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8554 (mm-30) REVERT: 5 599 MET cc_start: 0.8890 (mpp) cc_final: 0.8346 (mpp) REVERT: 5 639 MET cc_start: 0.8582 (mpp) cc_final: 0.7436 (mpp) REVERT: 5 640 TYR cc_start: 0.5434 (t80) cc_final: 0.5133 (t80) REVERT: 5 643 CYS cc_start: 0.8827 (m) cc_final: 0.8008 (t) REVERT: 5 664 ARG cc_start: 0.7532 (mpp-170) cc_final: 0.7291 (mtm-85) REVERT: 5 673 PHE cc_start: 0.8857 (t80) cc_final: 0.8493 (t80) REVERT: 5 693 LYS cc_start: 0.6375 (pttt) cc_final: 0.6168 (pttm) outliers start: 5 outliers final: 1 residues processed: 1461 average time/residue: 1.3766 time to fit residues: 3475.5245 Evaluate side-chains 1184 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1183 time to evaluate : 7.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 727 optimal weight: 20.0000 chunk 1171 optimal weight: 0.7980 chunk 714 optimal weight: 20.0000 chunk 555 optimal weight: 2.9990 chunk 814 optimal weight: 10.0000 chunk 1228 optimal weight: 10.0000 chunk 1130 optimal weight: 0.9980 chunk 978 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 755 optimal weight: 30.0000 chunk 599 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 343 GLN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS D 250 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN G 64 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 180 GLN O 184 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN Q 57 ASN R 121 HIS R 130 ASN ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN W 17 HIS X 93 ASN X 111 GLN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN e 34 ASN ** e 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN ** m 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 HIS ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 71 ASN ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 397 GLN ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 165109 Z= 0.273 Angle : 0.777 21.610 242524 Z= 0.390 Chirality : 0.042 0.389 30251 Planarity : 0.006 0.139 15718 Dihedral : 25.462 179.880 73507 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.03 % Favored : 90.45 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % 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: -1.72 (0.09), residues: 8227 helix: -0.07 (0.09), residues: 3243 sheet: -1.34 (0.16), residues: 893 loop : -2.00 (0.09), residues: 4091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP I 171 HIS 0.022 0.002 HIS 5 267 PHE 0.046 0.003 PHE x 182 TYR 0.044 0.003 TYR 5 392 ARG 0.015 0.001 ARG x 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16454 Ramachandran restraints generated. 8227 Oldfield, 0 Emsley, 8227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1396 time to evaluate : 7.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6518 (mm-30) REVERT: A 241 ARG cc_start: 0.7700 (mpt180) cc_final: 0.7061 (mpt180) REVERT: B 90 VAL cc_start: 0.7405 (p) cc_final: 0.6577 (p) REVERT: B 186 ASN cc_start: 0.6932 (t0) cc_final: 0.6635 (t0) REVERT: B 211 PHE cc_start: 0.3861 (m-80) cc_final: 0.3631 (m-80) REVERT: C 65 GLU cc_start: 0.9101 (tp30) cc_final: 0.8785 (pt0) REVERT: C 101 MET cc_start: 0.6067 (ptm) cc_final: 0.5710 (ptm) REVERT: C 161 TYR cc_start: 0.6491 (m-80) cc_final: 0.5861 (m-80) REVERT: C 320 LYS cc_start: 0.5247 (tptt) cc_final: 0.4930 (mmmt) REVERT: D 113 PHE cc_start: 0.7235 (m-80) cc_final: 0.6980 (m-80) REVERT: D 208 MET cc_start: 0.5941 (ttm) cc_final: 0.5597 (ttm) REVERT: D 242 LYS cc_start: 0.9065 (pttm) cc_final: 0.8780 (mmtm) REVERT: D 287 PHE cc_start: 0.7929 (m-80) cc_final: 0.7695 (m-80) REVERT: E 257 ILE cc_start: 0.8054 (pt) cc_final: 0.7467 (mt) REVERT: F 161 TYR cc_start: 0.6951 (m-80) cc_final: 0.6494 (m-80) REVERT: H 60 TRP cc_start: 0.4969 (m-90) cc_final: 0.4253 (m-90) REVERT: H 128 MET cc_start: 0.4859 (mmt) cc_final: 0.4493 (mmt) REVERT: I 153 ARG cc_start: 0.8337 (tmm-80) cc_final: 0.8010 (tmm-80) REVERT: J 175 LEU cc_start: 0.7868 (tp) cc_final: 0.7525 (tp) REVERT: L 8 MET cc_start: 0.7144 (mtt) cc_final: 0.5823 (ttp) REVERT: L 173 GLU cc_start: 0.7798 (pt0) cc_final: 0.7313 (tp30) REVERT: L 184 MET cc_start: 0.7378 (mmm) cc_final: 0.6913 (tpt) REVERT: N 32 GLN cc_start: 0.8405 (mp10) cc_final: 0.8105 (mm-40) REVERT: N 189 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7344 (ttm170) REVERT: O 87 MET cc_start: 0.6240 (mpp) cc_final: 0.5876 (mpp) REVERT: O 118 MET cc_start: 0.5992 (mpp) cc_final: 0.5494 (mtt) REVERT: P 82 ARG cc_start: 0.8280 (mmt90) cc_final: 0.7866 (mmt-90) REVERT: P 147 GLU cc_start: 0.3842 (tm-30) cc_final: 0.3612 (tm-30) REVERT: Q 87 THR cc_start: 0.8339 (p) cc_final: 0.7968 (p) REVERT: R 27 ASN cc_start: 0.8368 (m-40) cc_final: 0.8121 (m-40) REVERT: R 89 MET cc_start: 0.6850 (ttt) cc_final: 0.6190 (ptp) REVERT: S 52 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7496 (mmtt) REVERT: T 31 MET cc_start: 0.6315 (mpp) cc_final: 0.5243 (mpp) REVERT: T 159 MET cc_start: 0.6428 (pmm) cc_final: 0.4796 (mtt) REVERT: U 34 MET cc_start: 0.6765 (ppp) cc_final: 0.6094 (ppp) REVERT: V 112 MET cc_start: 0.8287 (ttm) cc_final: 0.8019 (ttm) REVERT: X 68 ARG cc_start: 0.6222 (ppt170) cc_final: 0.5347 (tmm160) REVERT: Y 14 ASN cc_start: 0.8168 (m110) cc_final: 0.7007 (t0) REVERT: Y 62 TYR cc_start: 0.7467 (m-80) cc_final: 0.7100 (m-10) REVERT: Y 70 VAL cc_start: 0.7780 (t) cc_final: 0.7161 (m) REVERT: Y 83 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7738 (mt-10) REVERT: Z 47 ASP cc_start: 0.7588 (t0) cc_final: 0.7217 (t70) REVERT: Z 73 LYS cc_start: 0.6320 (mmtt) cc_final: 0.6050 (mmtm) REVERT: Z 111 ARG cc_start: 0.8519 (mmt90) cc_final: 0.7166 (tpp80) REVERT: Z 116 VAL cc_start: 0.8771 (t) cc_final: 0.8401 (p) REVERT: a 10 LYS cc_start: 0.7462 (mmtp) cc_final: 0.7182 (mmtp) REVERT: a 58 MET cc_start: 0.5605 (mpp) cc_final: 0.5219 (mpp) REVERT: b 43 MET cc_start: 0.5658 (tpt) cc_final: 0.5107 (tpp) REVERT: b 57 MET cc_start: 0.2390 (ttm) cc_final: 0.2002 (tpt) REVERT: b 65 MET cc_start: 0.7181 (mmp) cc_final: 0.6491 (tmm) REVERT: c 21 VAL cc_start: 0.8050 (t) cc_final: 0.7802 (t) REVERT: c 74 TYR cc_start: 0.5933 (t80) cc_final: 0.5607 (t80) REVERT: c 81 LEU cc_start: 0.7288 (tp) cc_final: 0.7085 (tp) REVERT: d 67 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7705 (mmp80) REVERT: e 69 MET cc_start: 0.7655 (ppp) cc_final: 0.7191 (ttp) REVERT: e 88 LEU cc_start: 0.6301 (tp) cc_final: 0.6072 (tt) REVERT: e 98 GLU cc_start: 0.6682 (mp0) cc_final: 0.6259 (mp0) REVERT: g 5 LEU cc_start: 0.8394 (pt) cc_final: 0.8192 (pt) REVERT: g 18 ASN cc_start: 0.8562 (t0) cc_final: 0.8252 (t0) REVERT: h 22 ASP cc_start: 0.5638 (t0) cc_final: 0.5436 (t0) REVERT: h 44 LEU cc_start: 0.8467 (mt) cc_final: 0.8221 (mt) REVERT: h 52 LYS cc_start: 0.8170 (mptt) cc_final: 0.7685 (tptt) REVERT: i 82 ARG cc_start: 0.3695 (mtt180) cc_final: 0.3219 (mtt180) REVERT: j 32 SER cc_start: 0.9441 (m) cc_final: 0.9048 (p) REVERT: j 50 SER cc_start: 0.9254 (p) cc_final: 0.8948 (p) REVERT: j 54 LYS cc_start: 0.8794 (ptmt) cc_final: 0.8522 (pttm) REVERT: n 14 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7948 (mmtt) REVERT: o 28 LYS cc_start: 0.5668 (mmpt) cc_final: 0.4694 (mmmt) REVERT: o 82 MET cc_start: 0.4874 (mmm) cc_final: 0.4572 (mmm) REVERT: o 91 PHE cc_start: 0.7197 (t80) cc_final: 0.6850 (t80) REVERT: p 31 ILE cc_start: 0.8550 (mm) cc_final: 0.8246 (tp) REVERT: r 97 ILE cc_start: 0.7388 (pt) cc_final: 0.7181 (tp) REVERT: r 125 MET cc_start: 0.2220 (pmm) cc_final: 0.0867 (mmm) REVERT: s 60 MET cc_start: 0.1560 (mtp) cc_final: 0.1328 (mmm) REVERT: s 95 LEU cc_start: -0.1019 (pp) cc_final: -0.1360 (pp) REVERT: x 54 MET cc_start: 0.8545 (mmp) cc_final: 0.7900 (mmm) REVERT: x 160 LEU cc_start: 0.9267 (mt) cc_final: 0.9037 (mt) REVERT: x 163 LEU cc_start: 0.9204 (mt) cc_final: 0.8795 (mt) REVERT: x 166 ASP cc_start: 0.9232 (m-30) cc_final: 0.9020 (m-30) REVERT: x 167 GLU cc_start: 0.8847 (mt-10) cc_final: 0.7677 (tm-30) REVERT: x 168 LEU cc_start: 0.9000 (mt) cc_final: 0.8800 (mt) REVERT: x 171 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8539 (mmtt) REVERT: x 389 ASP cc_start: 0.8015 (m-30) cc_final: 0.7597 (m-30) REVERT: x 392 LYS cc_start: 0.9474 (mmtm) cc_final: 0.9136 (mmtm) REVERT: x 401 MET cc_start: 0.6851 (ptt) cc_final: 0.6434 (ptt) REVERT: x 415 ARG cc_start: 0.8343 (ptp90) cc_final: 0.7969 (ptp90) REVERT: y 35 LYS cc_start: 0.8530 (tptp) cc_final: 0.8219 (tptp) REVERT: y 38 MET cc_start: 0.6564 (ttt) cc_final: 0.5943 (mmt) REVERT: z 76 MET cc_start: 0.8279 (ptp) cc_final: 0.7520 (tpt) REVERT: z 79 LEU cc_start: 0.8381 (tt) cc_final: 0.8172 (tt) REVERT: 1 451 PHE cc_start: 0.8364 (t80) cc_final: 0.8060 (t80) REVERT: 1 455 ILE cc_start: 0.9281 (mt) cc_final: 0.8992 (mt) REVERT: 1 458 ARG cc_start: 0.6225 (ttt180) cc_final: 0.5570 (mtt90) REVERT: 4 12 ASN cc_start: 0.8875 (m-40) cc_final: 0.8576 (m110) REVERT: 5 1 MET cc_start: -0.0569 (ttp) cc_final: -0.1875 (mtm) REVERT: 5 78 TYR cc_start: 0.8876 (t80) cc_final: 0.8156 (t80) REVERT: 5 114 ASN cc_start: 0.8754 (m110) cc_final: 0.7874 (m110) REVERT: 5 118 PHE cc_start: 0.8398 (m-10) cc_final: 0.8066 (m-10) REVERT: 5 192 ILE cc_start: 0.8387 (mm) cc_final: 0.8107 (mm) REVERT: 5 357 TRP cc_start: 0.9107 (p-90) cc_final: 0.8763 (p-90) REVERT: 5 418 SER cc_start: 0.9508 (m) cc_final: 0.9145 (p) REVERT: 5 431 LYS cc_start: 0.9200 (ptpp) cc_final: 0.8927 (ptpp) REVERT: 5 461 ILE cc_start: 0.9188 (mt) cc_final: 0.8625 (mt) REVERT: 5 469 ILE cc_start: 0.9472 (pt) cc_final: 0.9247 (tp) REVERT: 5 483 TYR cc_start: 0.8774 (m-80) cc_final: 0.8307 (m-80) REVERT: 5 511 TRP cc_start: 0.7284 (t60) cc_final: 0.6485 (m100) REVERT: 5 523 MET cc_start: 0.7690 (mtp) cc_final: 0.7389 (mmm) REVERT: 5 541 LEU cc_start: 0.9240 (mp) cc_final: 0.9020 (mp) REVERT: 5 568 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8518 (mm-30) REVERT: 5 639 MET cc_start: 0.8567 (mpp) cc_final: 0.7702 (mpp) REVERT: 5 640 TYR cc_start: 0.5772 (t80) cc_final: 0.5567 (t80) REVERT: 5 643 CYS cc_start: 0.8711 (m) cc_final: 0.8044 (t) outliers start: 3 outliers final: 0 residues processed: 1396 average time/residue: 1.3862 time to fit residues: 3347.0991 Evaluate side-chains 1136 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1136 time to evaluate : 7.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1233 random chunks: chunk 776 optimal weight: 20.0000 chunk 1041 optimal weight: 20.0000 chunk 299 optimal weight: 1.9990 chunk 901 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 chunk 271 optimal weight: 7.9990 chunk 979 optimal weight: 10.0000 chunk 410 optimal weight: 0.8980 chunk 1006 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 282 HIS C 343 GLN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 HIS L 28 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** P 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN R 130 ASN ** T 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 GLN Y 20 ASN ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 34 ASN ** e 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 HIS ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 397 GLN ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.153246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.139730 restraints weight = 520155.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.136716 restraints weight = 444759.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.134655 restraints weight = 385950.094| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 165109 Z= 0.226 Angle : 0.733 20.671 242524 Z= 0.369 Chirality : 0.040 0.311 30251 Planarity : 0.006 0.138 15718 Dihedral : 25.418 179.997 73507 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.24 % Favored : 91.24 % Rotamer: Outliers : 0.06 % Allowed : 0.53 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.04 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.09), residues: 8227 helix: 0.02 (0.09), residues: 3244 sheet: -1.27 (0.16), residues: 899 loop : -1.94 (0.09), residues: 4084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 171 HIS 0.020 0.001 HIS 5 267 PHE 0.047 0.002 PHE x 182 TYR 0.045 0.002 TYR x 364 ARG 0.033 0.001 ARG V 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51790.75 seconds wall clock time: 902 minutes 45.70 seconds (54165.70 seconds total)