Starting phenix.real_space_refine on Thu Mar 28 00:14:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftj_4317/03_2024/6ftj_4317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftj_4317/03_2024/6ftj_4317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftj_4317/03_2024/6ftj_4317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftj_4317/03_2024/6ftj_4317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftj_4317/03_2024/6ftj_4317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftj_4317/03_2024/6ftj_4317_updated.pdb" } resolution = 4.7 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= 0.008 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 3937 5.49 5 Mg 159 5.21 5 S 319 5.16 5 C 80491 2.51 5 N 28299 2.21 5 O 38901 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 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 152111 Number of models: 1 Model: "" Number of chains: 74 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: "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: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 882 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'UNK:plan-1': 26, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 191 Chain: "2" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 300 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'TRANS': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'UNK:plan-1': 60} Unresolved non-hydrogen planarities: 60 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: "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: 57.91, per 1000 atoms: 0.38 Number of scatterers: 152111 At special positions: 0 Unit cell: (244.442, 294.523, 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 3937 15.00 Mg 159 11.99 O 38901 8.00 N 28299 7.00 C 80491 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 95739 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: 65.95 Conformation dependent library (CDL) restraints added in 9.0 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 16282 Ramachandran restraints generated. 8141 Oldfield, 0 Emsley, 8141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15970 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: 301 helices and 67 sheets defined 48.5% alpha, 11.7% beta 1206 base pairs and 1914 stacking pairs defined. Time for finding SS restraints: 84.66 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: 6.030A pdb=" N ILE x 9 " --> pdb=" O PHE x 5 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.539A 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: 3.830A pdb=" N VAL x 162 " --> pdb=" O ALA x 158 " (cutoff:3.500A) removed outlier: 3.770A 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: 5.051A 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: 4.191A pdb=" N PHE x 261 " --> pdb=" O TYR x 257 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG x 262 " --> pdb=" O PHE x 258 " (cutoff:3.500A) Processing helix chain 'x' and resid 291 through 312 removed outlier: 3.978A 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: 4.310A 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: 3.866A 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: 5.549A pdb=" N GLU x 381 " --> pdb=" O LYS x 377 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL x 382 " --> pdb=" O THR x 378 " (cutoff:3.500A) removed outlier: 3.731A 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: 4.794A 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: 4.795A 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: 3.618A 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: 3.708A 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: 4.269A 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: 3.540A pdb=" N PHE y 33 " --> pdb=" O ASP y 29 " (cutoff:3.500A) removed outlier: 4.022A 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: 4.333A 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: 3.775A pdb=" N GLY z 91 " --> pdb=" O LEU z 87 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS z 92 " --> pdb=" O HIS z 88 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR z 94 " --> pdb=" O TRP z 90 " (cutoff:3.500A) removed outlier: 3.913A 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 MET 1 473 " --> pdb=" O ALA 1 469 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG 1 502 " --> pdb=" O GLU 1 498 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR 1 503 " --> pdb=" O THR 1 499 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS 1 504 " --> pdb=" O ILE 1 500 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN 1 505 " --> pdb=" O ASN 1 501 " (cutoff:3.500A) Processing helix chain '1' and resid 509 through 539 removed outlier: 4.255A pdb=" N LYS 1 538 " --> pdb=" O GLN 1 534 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR 1 539 " --> pdb=" O SER 1 535 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 573 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: 3.979A 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: 3.631A pdb=" N GLY 3 47 " --> pdb=" O LEU 3 43 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE 3 48 " --> pdb=" O ILE 3 44 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE 3 49 " --> pdb=" O THR 3 45 " (cutoff:3.500A) removed outlier: 5.396A 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: 3.512A 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: 3.567A 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: 3.511A 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: 3.564A 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: 3.928A pdb=" N PHE 5 31 " --> pdb=" O ALA 5 27 " (cutoff:3.500A) removed outlier: 4.024A 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: 5.299A 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: 5.062A 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: 3.547A pdb=" N ALA 5 61 " --> pdb=" O THR 5 57 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 88 removed outlier: 5.153A 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: 4.443A pdb=" N HIS 5 104 " --> pdb=" O TYR 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 111 through 139 removed outlier: 4.104A 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: 4.070A 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: 4.743A pdb=" N ALA 5 149 " --> pdb=" O LEU 5 145 " (cutoff:3.500A) removed outlier: 3.530A 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: 4.873A 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: 5.602A 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: 3.630A 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: 4.297A 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: 5.140A pdb=" N SER 5 255 " --> pdb=" O SER 5 251 " (cutoff:3.500A) Processing helix chain '5' and resid 259 through 264 removed outlier: 3.513A 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: 3.701A 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: 4.428A 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: 4.012A 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: 3.704A 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: 3.690A 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: 4.627A 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: 4.009A 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: 3.702A 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: 3.617A 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: 4.565A 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: 3.613A pdb=" N ILE 5 532 " --> pdb=" O TYR 5 528 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR 5 533 " --> pdb=" O GLY 5 529 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET 5 535 " --> pdb=" O GLN 5 531 " (cutoff:3.500A) Processing helix chain '5' and resid 548 through 560 removed outlier: 4.090A 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: 5.185A 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: 3.845A pdb=" N ARG 5 690 " --> pdb=" O VAL 5 580 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU 5 688 " --> pdb=" O PHE 5 582 " (cutoff:3.500A) 2696 hydrogen bonds defined for protein. 7992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3167 hydrogen bonds 5520 hydrogen bond angles 0 basepair planarities 1206 basepair parallelities 1914 stacking parallelities Total time for adding SS restraints: 299.99 Time building geometry restraints manager: 70.92 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: 18483 1.32 - 1.73: 144171 1.73 - 2.14: 521 2.14 - 2.55: 1 2.55 - 2.97: 6 Bond restraints: 163182 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 163177 not shown) Histogram of bond angle deviations from ideal: 60.46 - 81.84: 6 81.84 - 103.23: 11694 103.23 - 124.62: 210578 124.62 - 146.00: 17264 146.00 - 167.39: 2 Bond angle restraints: 239544 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 60.46 62.13 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 79.43 42.11 1.91e+00 2.74e-01 4.86e+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 239539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 91700 35.92 - 71.85: 11721 71.85 - 107.77: 1445 107.77 - 143.69: 84 143.69 - 179.61: 127 Dihedral angle restraints: 105077 sinusoidal: 80328 harmonic: 24749 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 -122.11 -57.89 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 105074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 26074 0.164 - 0.328: 3612 0.328 - 0.493: 110 0.493 - 0.657: 40 0.657 - 0.821: 9 Chirality restraints: 29845 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 29842 not shown) Planarity restraints: 15620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER 5 590 " -0.173 2.00e-02 2.50e+03 2.51e-01 6.32e+02 pdb=" C SER 5 590 " 0.384 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 1.15e+02 pdb=" C ILE 5 532 " -0.186 2.00e-02 2.50e+03 pdb=" O ILE 5 532 " 0.068 2.00e-02 2.50e+03 pdb=" N THR 5 533 " 0.058 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 15617 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.36: 32 1.36 - 2.24: 337 2.24 - 3.13: 116483 3.13 - 4.01: 485673 4.01 - 4.90: 781946 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1384471 Sorted by model distance: nonbonded pdb=" CB GLU X 84 " pdb=" CG HIS x 404 " model vdw 0.475 3.660 nonbonded pdb=" O3' U u2432 " pdb=" NZ LYS x 268 " model vdw 0.509 2.520 nonbonded pdb=" CA VAL z 73 " pdb=" CE MET z 76 " model vdw 0.639 3.890 nonbonded pdb=" CA GLU X 84 " pdb=" CD2 HIS x 404 " model vdw 0.666 3.690 nonbonded pdb=" C GLU X 84 " pdb=" NE2 HIS x 404 " model vdw 0.667 3.350 ... (remaining 1384466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.270 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: 29.870 Check model and map are aligned: 1.600 Set scattering table: 1.020 Process input model: 640.010 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.390 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: 0.030 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 688.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 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 163182 Z= 0.674 Angle : 1.387 62.135 239544 Z= 0.906 Chirality : 0.103 0.821 29845 Planarity : 0.009 0.251 15619 Dihedral : 25.542 179.613 89107 Min Nonbonded Distance : 0.475 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 2.37 % Allowed : 9.80 % Favored : 87.83 % Rotamer: Outliers : 11.77 % Allowed : 12.51 % Favored : 75.73 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.48 % 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: -4.05 (0.08), residues: 8141 helix: -2.27 (0.07), residues: 3111 sheet: -3.20 (0.13), residues: 930 loop : -2.90 (0.08), residues: 4100 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 0.046 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) ************************************************ 16282 Ramachandran restraints generated. 8141 Oldfield, 0 Emsley, 8141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16282 Ramachandran restraints generated. 8141 Oldfield, 0 Emsley, 8141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3343 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 814 poor density : 2529 time to evaluate : 7.626 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 158 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8896 (mm) REVERT: A 162 ASN cc_start: 0.5339 (p0) cc_final: 0.5032 (p0) REVERT: A 165 VAL cc_start: 0.7854 (OUTLIER) cc_final: 0.5532 (m) REVERT: A 199 VAL cc_start: 0.9442 (t) cc_final: 0.9125 (t) REVERT: A 204 MET cc_start: 0.8768 (mtt) cc_final: 0.8555 (mtp) REVERT: A 207 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8821 (p) REVERT: A 215 ASN cc_start: 0.9136 (m-40) cc_final: 0.8860 (m-40) REVERT: A 219 ILE cc_start: 0.8530 (mt) cc_final: 0.8217 (mt) REVERT: A 226 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6463 (ptt180) REVERT: B 153 MET cc_start: 0.7909 (mtp) cc_final: 0.7374 (mmm) REVERT: B 244 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 262 VAL cc_start: 0.6500 (OUTLIER) cc_final: 0.6142 (p) REVERT: B 329 ASP cc_start: -0.3313 (OUTLIER) cc_final: -0.4661 (m-30) REVERT: B 351 LEU cc_start: 0.7774 (mm) cc_final: 0.7467 (mt) REVERT: B 352 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7383 (tt) REVERT: B 383 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: B 389 MET cc_start: 0.6810 (mmm) cc_final: 0.6457 (tpt) REVERT: C 65 GLU cc_start: 0.9332 (tp30) cc_final: 0.8905 (tp30) REVERT: C 97 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7337 (ttp80) REVERT: C 101 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5285 (ptm) REVERT: C 108 TRP cc_start: 0.6177 (p90) cc_final: 0.5758 (p90) REVERT: C 114 ARG cc_start: 0.0495 (OUTLIER) cc_final: 0.0062 (ptt180) REVERT: C 274 LYS cc_start: 0.6198 (mttp) cc_final: 0.5913 (mttm) REVERT: D 234 ASP cc_start: 0.8681 (m-30) cc_final: 0.7881 (t0) REVERT: D 239 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.3797 (tmm) REVERT: D 256 LYS cc_start: 0.3959 (OUTLIER) cc_final: 0.3049 (mptt) REVERT: E 124 HIS cc_start: 0.3369 (OUTLIER) cc_final: 0.2572 (m-70) REVERT: E 136 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4796 (tt) REVERT: E 208 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4397 (pp) REVERT: F 211 TRP cc_start: 0.6144 (t-100) cc_final: 0.5377 (t-100) REVERT: F 249 MET cc_start: 0.3320 (mtm) cc_final: 0.2684 (ttp) REVERT: I 43 VAL cc_start: 0.6423 (OUTLIER) cc_final: 0.5559 (m) REVERT: I 115 MET cc_start: 0.7321 (tpt) cc_final: 0.6479 (tpp) REVERT: I 116 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6080 (ptt180) REVERT: J 90 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7404 (mmt90) REVERT: L 8 MET cc_start: 0.5228 (mtt) cc_final: 0.4476 (mtp) REVERT: L 94 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8565 (mm) REVERT: L 126 LEU cc_start: 0.8267 (tp) cc_final: 0.7853 (tt) REVERT: L 143 GLU cc_start: 0.3336 (OUTLIER) cc_final: 0.2424 (tt0) REVERT: L 175 ASN cc_start: 0.6211 (t0) cc_final: 0.5836 (t0) REVERT: M 4 ARG cc_start: 0.2708 (OUTLIER) cc_final: 0.0976 (ptt180) REVERT: M 53 LYS cc_start: 0.4287 (OUTLIER) cc_final: 0.3825 (mtpt) REVERT: N 26 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5037 (mpt-90) REVERT: N 134 LEU cc_start: 0.6326 (mt) cc_final: 0.5216 (mt) REVERT: O 5 GLN cc_start: 0.3626 (OUTLIER) cc_final: 0.2180 (mt0) REVERT: O 66 PRO cc_start: 0.6717 (Cg_exo) cc_final: 0.5893 (Cg_endo) REVERT: O 80 PHE cc_start: 0.6124 (t80) cc_final: 0.5655 (t80) REVERT: O 85 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6738 (ttt-90) REVERT: O 118 MET cc_start: 0.6372 (mmp) cc_final: 0.4653 (mmm) REVERT: P 4 TYR cc_start: 0.6889 (m-10) cc_final: 0.5632 (m-10) REVERT: P 48 LEU cc_start: 0.8492 (mt) cc_final: 0.8168 (mt) REVERT: P 50 ASP cc_start: 0.7659 (m-30) cc_final: 0.7269 (m-30) REVERT: P 100 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.5582 (t) REVERT: P 118 GLN cc_start: 0.1703 (OUTLIER) cc_final: 0.0476 (tp40) REVERT: P 121 LYS cc_start: 0.8626 (mttt) cc_final: 0.8349 (mtmm) REVERT: Q 29 VAL cc_start: 0.7899 (t) cc_final: 0.7427 (t) REVERT: R 7 GLN cc_start: 0.8702 (mp10) cc_final: 0.7993 (mm-40) REVERT: R 40 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: R 89 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7301 (ttm) REVERT: R 113 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5935 (mmmt) REVERT: S 10 TYR cc_start: 0.5357 (m-80) cc_final: 0.4695 (m-80) REVERT: S 48 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7655 (p) REVERT: S 165 PRO cc_start: 0.3863 (Cg_exo) cc_final: 0.2955 (Cg_endo) REVERT: T 36 LYS cc_start: 0.7514 (mtmt) cc_final: 0.7154 (pttm) REVERT: T 74 ILE cc_start: 0.6486 (tt) cc_final: 0.5959 (pt) REVERT: T 89 ILE cc_start: 0.5277 (pt) cc_final: 0.4770 (pt) REVERT: T 152 GLU cc_start: 0.3572 (OUTLIER) cc_final: 0.3028 (mt-10) REVERT: U 85 TYR cc_start: 0.6386 (t80) cc_final: 0.5075 (t80) REVERT: U 114 TYR cc_start: 0.5641 (m-80) cc_final: 0.5366 (m-80) REVERT: V 27 ASN cc_start: 0.8062 (p0) cc_final: 0.7151 (t0) REVERT: V 35 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8178 (tptt) REVERT: V 84 GLN cc_start: 0.6691 (pt0) cc_final: 0.6258 (pm20) REVERT: V 86 LYS cc_start: 0.7445 (tptt) cc_final: 0.6270 (tptt) REVERT: V 123 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7832 (mmmt) REVERT: W 13 ILE cc_start: 0.7162 (mt) cc_final: 0.6803 (mt) REVERT: W 43 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7598 (pttm) REVERT: X 131 ASP cc_start: 0.8465 (m-30) cc_final: 0.8186 (t0) REVERT: Y 7 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8461 (t) REVERT: a 7 LYS cc_start: 0.6804 (tttt) cc_final: 0.6404 (mttt) REVERT: a 10 LYS cc_start: 0.7252 (mptm) cc_final: 0.6995 (mptm) REVERT: a 63 LEU cc_start: 0.9221 (tt) cc_final: 0.8902 (mt) REVERT: a 84 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4686 (tp30) REVERT: a 120 GLN cc_start: 0.6859 (tp40) cc_final: 0.6519 (pt0) REVERT: b 28 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.4707 (ttm170) REVERT: b 57 MET cc_start: 0.0808 (ttm) cc_final: -0.0351 (mmm) REVERT: c 78 ASN cc_start: 0.6232 (OUTLIER) cc_final: 0.4870 (p0) REVERT: c 91 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8829 (t) REVERT: d 19 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: d 23 ARG cc_start: 0.1080 (OUTLIER) cc_final: 0.0523 (ptp-170) REVERT: d 39 LYS cc_start: 0.7404 (mptp) cc_final: 0.7082 (mmmt) REVERT: d 61 ASP cc_start: 0.8784 (t0) cc_final: 0.8306 (p0) REVERT: d 94 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.4810 (pt0) REVERT: e 37 LYS cc_start: 0.7044 (ttmm) cc_final: 0.6546 (ttmm) REVERT: e 49 PHE cc_start: 0.7444 (m-80) cc_final: 0.6636 (m-10) REVERT: f 36 ARG cc_start: 0.1431 (OUTLIER) cc_final: 0.0922 (tpt-90) REVERT: f 64 PRO cc_start: -0.0008 (OUTLIER) cc_final: -0.0682 (Cg_endo) REVERT: f 69 VAL cc_start: 0.3818 (OUTLIER) cc_final: 0.3606 (m) REVERT: g 33 LEU cc_start: 0.8482 (mt) cc_final: 0.8220 (mt) REVERT: h 17 LEU cc_start: 0.8372 (mt) cc_final: 0.8143 (mt) REVERT: h 20 GLN cc_start: 0.8600 (tt0) cc_final: 0.8017 (tt0) REVERT: h 50 VAL cc_start: 0.8805 (t) cc_final: 0.8543 (p) REVERT: h 54 ILE cc_start: 0.9192 (mt) cc_final: 0.8733 (mt) REVERT: h 58 LEU cc_start: 0.8886 (mt) cc_final: 0.8677 (tp) REVERT: h 83 LEU cc_start: 0.8914 (mt) cc_final: 0.8413 (mp) REVERT: i 33 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.6034 (tt) REVERT: j 15 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8468 (p) REVERT: j 28 HIS cc_start: 0.8468 (t-170) cc_final: 0.8172 (t-170) REVERT: j 47 TYR cc_start: 0.8224 (m-80) cc_final: 0.7436 (m-80) REVERT: j 56 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7841 (ptp-110) REVERT: j 57 ASN cc_start: 0.7321 (p0) cc_final: 0.7006 (t0) REVERT: j 68 LYS cc_start: 0.8920 (ptmm) cc_final: 0.8628 (tppt) REVERT: k 66 VAL cc_start: 0.5002 (OUTLIER) cc_final: 0.4624 (t) REVERT: k 70 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.5595 (mmtt) REVERT: l 18 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8539 (tmtt) REVERT: l 26 TRP cc_start: 0.7791 (p-90) cc_final: 0.6679 (p-90) REVERT: l 27 ILE cc_start: 0.8144 (mm) cc_final: 0.7459 (mm) REVERT: l 48 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8547 (mmmt) REVERT: m 85 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6177 (mt) REVERT: n 4 LYS cc_start: 0.7597 (tttt) cc_final: 0.7240 (ptpp) REVERT: n 14 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8286 (mmtt) REVERT: o 36 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6834 (pp30) REVERT: o 103 VAL cc_start: 0.5670 (t) cc_final: 0.5084 (t) REVERT: p 47 MET cc_start: 0.6374 (mmt) cc_final: 0.6066 (tpt) REVERT: p 79 VAL cc_start: 0.7456 (t) cc_final: 0.6855 (p) REVERT: r 103 HIS cc_start: 0.3875 (OUTLIER) cc_final: 0.2870 (t-90) REVERT: s 101 MET cc_start: 0.8500 (mmm) cc_final: 0.7866 (tmm) REVERT: s 177 MET cc_start: 0.3725 (mmm) cc_final: 0.3280 (mtt) REVERT: s 191 GLN cc_start: 0.2820 (OUTLIER) cc_final: 0.2317 (pm20) REVERT: t 12 VAL cc_start: 0.2027 (t) cc_final: 0.1759 (m) REVERT: t 104 ILE cc_start: 0.2978 (OUTLIER) cc_final: 0.2290 (mp) REVERT: x 169 LEU cc_start: 0.8369 (mt) cc_final: 0.7990 (mt) REVERT: x 189 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8521 (mt-10) REVERT: x 245 LEU cc_start: 0.9263 (tt) cc_final: 0.8997 (mm) REVERT: x 396 GLU cc_start: 0.8729 (tt0) cc_final: 0.8456 (tp30) REVERT: x 462 VAL cc_start: 0.5900 (OUTLIER) cc_final: 0.5686 (p) REVERT: y 24 ARG cc_start: 0.7957 (tpt90) cc_final: 0.7613 (tpt90) REVERT: y 38 MET cc_start: 0.8616 (ttp) cc_final: 0.8387 (tpp) REVERT: 3 41 TYR cc_start: 0.8380 (t80) cc_final: 0.8043 (t80) REVERT: 3 90 SER cc_start: 0.7622 (OUTLIER) cc_final: 0.6462 (m) REVERT: 5 16 THR cc_start: 0.8950 (m) cc_final: 0.8551 (p) REVERT: 5 21 LEU cc_start: 0.9131 (tm) cc_final: 0.8278 (tm) REVERT: 5 50 PRO cc_start: 0.8847 (Cg_exo) cc_final: 0.8616 (Cg_endo) REVERT: 5 57 THR cc_start: 0.9432 (m) cc_final: 0.9230 (m) REVERT: 5 93 MET cc_start: 0.8314 (mtm) cc_final: 0.7869 (ttm) REVERT: 5 146 LEU cc_start: 0.8212 (pp) cc_final: 0.7997 (pp) REVERT: 5 252 MET cc_start: 0.7712 (tpp) cc_final: 0.7369 (tpp) REVERT: 5 371 PHE cc_start: 0.7761 (t80) cc_final: 0.7186 (t80) REVERT: 5 375 LEU cc_start: 0.9364 (tt) cc_final: 0.9094 (mt) REVERT: 5 376 TYR cc_start: 0.8481 (t80) cc_final: 0.8274 (t80) REVERT: 5 544 ASN cc_start: 0.7541 (m-40) cc_final: 0.7286 (m110) REVERT: 5 562 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7880 (p) REVERT: 5 597 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8355 (tp) REVERT: 5 639 MET cc_start: 0.6751 (tpp) cc_final: 0.6108 (tpp) REVERT: 5 643 CYS cc_start: 0.7739 (m) cc_final: 0.7405 (m) outliers start: 814 outliers final: 176 residues processed: 3035 average time/residue: 1.5841 time to fit residues: 7816.0844 Evaluate side-chains 1741 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1505 time to evaluate : 7.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 1033 optimal weight: 20.0000 chunk 927 optimal weight: 10.0000 chunk 514 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 625 optimal weight: 0.0970 chunk 495 optimal weight: 9.9990 chunk 959 optimal weight: 9.9990 chunk 371 optimal weight: 7.9990 chunk 583 optimal weight: 0.9990 chunk 714 optimal weight: 20.0000 chunk 1111 optimal weight: 7.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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** A 217 GLN B 68 ASN B 158 GLN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN C 212 ASN C 310 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS E 252 GLN E 280 HIS F 41 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN G 108 GLN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 HIS L 19 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN ** P 40 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** Q 21 GLN Q 188 ASN R 39 GLN R 40 GLN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN S 50 GLN S 92 ASN S 122 HIS S 125 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 HIS W 17 HIS W 30 GLN W 50 ASN W 59 HIS X 57 GLN X 105 ASN X 111 GLN Y 72 GLN a 17 HIS a 44 ASN a 60 HIS a 89 ASN b 58 GLN e 24 GLN e 43 ASN e 102 ASN e 107 ASN h 98 HIS i 15 HIS i 80 HIS j 30 GLN ** j 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN m 104 HIS o 36 GLN ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 HIS ** r 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 GLN s 72 ASN s 105 ASN x 154 GLN x 186 ASN ** x 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 ASN y 62 ASN 4 12 ASN ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 531 GLN 5 686 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 163182 Z= 0.300 Angle : 0.922 20.405 239544 Z= 0.467 Chirality : 0.048 0.397 29845 Planarity : 0.008 0.264 15619 Dihedral : 25.783 179.956 72307 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.12 % Favored : 92.08 % Rotamer: Outliers : 0.48 % Allowed : 6.16 % Favored : 93.36 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.78 % Twisted General : 0.31 % 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: -2.26 (0.09), residues: 8147 helix: -0.40 (0.09), residues: 3208 sheet: -2.39 (0.15), residues: 894 loop : -2.21 (0.09), residues: 4045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP 5 71 HIS 0.017 0.002 HIS 5 615 PHE 0.075 0.003 PHE 5 256 TYR 0.049 0.003 TYR C 161 ARG 0.025 0.001 ARG h 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1873 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1840 time to evaluate : 7.627 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 158 ILE cc_start: 0.9040 (mt) cc_final: 0.8829 (mp) REVERT: A 162 ASN cc_start: 0.6242 (p0) cc_final: 0.5857 (p0) REVERT: A 196 TRP cc_start: 0.8331 (t60) cc_final: 0.7653 (t60) REVERT: A 204 MET cc_start: 0.8826 (mtt) cc_final: 0.8327 (mtm) REVERT: B 383 GLU cc_start: 0.8621 (pp20) cc_final: 0.8368 (pm20) REVERT: C 95 MET cc_start: 0.8363 (ptp) cc_final: 0.8068 (ptm) REVERT: C 284 MET cc_start: 0.7116 (ttp) cc_final: 0.5961 (tmm) REVERT: D 157 ASN cc_start: 0.8293 (t0) cc_final: 0.7744 (t0) REVERT: D 235 MET cc_start: 0.6099 (ptm) cc_final: 0.5155 (ptm) REVERT: D 244 HIS cc_start: 0.7163 (m90) cc_final: 0.6935 (m90) REVERT: F 211 TRP cc_start: 0.6272 (t-100) cc_final: 0.5154 (t60) REVERT: H 128 MET cc_start: 0.5379 (mmp) cc_final: 0.4940 (mmm) REVERT: I 115 MET cc_start: 0.6729 (tpt) cc_final: 0.6265 (tpp) REVERT: J 67 LYS cc_start: 0.7955 (mppt) cc_final: 0.7682 (pttt) REVERT: J 90 ARG cc_start: 0.7851 (tpt170) cc_final: 0.7573 (tpt170) REVERT: J 163 MET cc_start: 0.6752 (ppp) cc_final: 0.6370 (ppp) REVERT: L 8 MET cc_start: 0.5251 (mtt) cc_final: 0.3913 (mtp) REVERT: L 20 ARG cc_start: 0.8665 (ptm160) cc_final: 0.8165 (ptm160) REVERT: L 184 MET cc_start: 0.7589 (mmm) cc_final: 0.7177 (mmm) REVERT: M 55 MET cc_start: 0.6292 (mmp) cc_final: 0.5270 (ttm) REVERT: M 83 ASN cc_start: 0.5534 (m-40) cc_final: 0.4843 (t0) REVERT: N 19 MET cc_start: 0.2324 (mmm) cc_final: 0.1711 (ttt) REVERT: O 118 MET cc_start: 0.6994 (mmp) cc_final: 0.5538 (mmm) REVERT: P 80 GLN cc_start: 0.6477 (mm110) cc_final: 0.6163 (mm110) REVERT: R 7 GLN cc_start: 0.9154 (mp10) cc_final: 0.8393 (mm-40) REVERT: R 30 ASN cc_start: 0.8979 (m110) cc_final: 0.8732 (p0) REVERT: R 66 ASN cc_start: 0.8428 (m-40) cc_final: 0.8224 (m110) REVERT: R 89 MET cc_start: 0.8039 (tpt) cc_final: 0.7493 (ttm) REVERT: R 113 LYS cc_start: 0.7240 (mptt) cc_final: 0.6958 (mmmt) REVERT: U 85 TYR cc_start: 0.6361 (t80) cc_final: 0.6098 (t80) REVERT: V 14 PHE cc_start: 0.8069 (m-80) cc_final: 0.7742 (m-80) REVERT: V 27 ASN cc_start: 0.8149 (p0) cc_final: 0.7424 (t0) REVERT: V 39 ILE cc_start: 0.9002 (mp) cc_final: 0.8677 (mp) REVERT: V 61 VAL cc_start: 0.8281 (p) cc_final: 0.7989 (p) REVERT: V 62 MET cc_start: 0.6973 (mpp) cc_final: 0.6609 (mpp) REVERT: V 86 LYS cc_start: 0.7628 (tptt) cc_final: 0.6764 (tptt) REVERT: V 105 ILE cc_start: 0.8788 (mp) cc_final: 0.8386 (mp) REVERT: V 113 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7746 (ptpp) REVERT: X 56 ARG cc_start: 0.8381 (mtt-85) cc_final: 0.7591 (mmm-85) REVERT: X 93 ASN cc_start: 0.7874 (m-40) cc_final: 0.7439 (t0) REVERT: X 94 ASN cc_start: 0.7798 (t0) cc_final: 0.7529 (t0) REVERT: X 98 PHE cc_start: 0.7558 (m-80) cc_final: 0.7348 (m-80) REVERT: X 128 ILE cc_start: 0.8560 (mm) cc_final: 0.8329 (mm) REVERT: X 131 ASP cc_start: 0.8503 (m-30) cc_final: 0.8270 (t0) REVERT: Y 17 ARG cc_start: 0.9067 (tpm170) cc_final: 0.8797 (tpp-160) REVERT: Y 53 ASP cc_start: 0.7834 (m-30) cc_final: 0.7190 (m-30) REVERT: Y 74 TYR cc_start: 0.6786 (t80) cc_final: 0.6423 (t80) REVERT: Y 94 THR cc_start: 0.7037 (p) cc_final: 0.6208 (p) REVERT: a 26 ARG cc_start: 0.8499 (mmt90) cc_final: 0.8201 (mmt-90) REVERT: a 58 MET cc_start: 0.4617 (tpt) cc_final: 0.3668 (mmm) REVERT: a 112 LEU cc_start: 0.8462 (mt) cc_final: 0.8161 (mp) REVERT: a 120 GLN cc_start: 0.6374 (tp40) cc_final: 0.6106 (pt0) REVERT: b 57 MET cc_start: 0.1274 (ttm) cc_final: -0.0185 (mmm) REVERT: d 61 ASP cc_start: 0.8896 (t0) cc_final: 0.7870 (p0) REVERT: d 77 ILE cc_start: 0.4672 (tt) cc_final: 0.3833 (tt) REVERT: e 69 MET cc_start: 0.6252 (ttm) cc_final: 0.4893 (mmp) REVERT: e 90 MET cc_start: 0.5492 (pmm) cc_final: 0.4455 (pmm) REVERT: g 6 THR cc_start: 0.8928 (p) cc_final: 0.8722 (t) REVERT: g 36 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7689 (tptt) REVERT: g 65 MET cc_start: 0.7936 (ttt) cc_final: 0.7733 (ttt) REVERT: g 82 MET cc_start: 0.5862 (ttt) cc_final: 0.5534 (ttt) REVERT: h 20 GLN cc_start: 0.8542 (tt0) cc_final: 0.8332 (tt0) REVERT: h 23 ASP cc_start: 0.7794 (m-30) cc_final: 0.7271 (m-30) REVERT: h 83 LEU cc_start: 0.8969 (mt) cc_final: 0.8277 (mp) REVERT: h 86 LYS cc_start: 0.7697 (tttt) cc_final: 0.7413 (ttmt) REVERT: l 5 LYS cc_start: 0.8791 (mttm) cc_final: 0.8152 (mtpt) REVERT: l 16 LYS cc_start: 0.9532 (mmtm) cc_final: 0.9216 (mmmm) REVERT: l 18 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8603 (tmtt) REVERT: l 38 ASN cc_start: 0.7962 (t0) cc_final: 0.7614 (t0) REVERT: l 46 ARG cc_start: 0.7870 (ptt-90) cc_final: 0.7656 (ptt180) REVERT: n 14 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8211 (mmtt) REVERT: o 36 GLN cc_start: 0.8439 (tp40) cc_final: 0.7232 (pp30) REVERT: p 47 MET cc_start: 0.6455 (mmt) cc_final: 0.6002 (tpp) REVERT: p 79 VAL cc_start: 0.7561 (t) cc_final: 0.7196 (p) REVERT: p 86 LEU cc_start: 0.7249 (mt) cc_final: 0.6931 (mt) REVERT: r 49 VAL cc_start: 0.6399 (t) cc_final: 0.5826 (t) REVERT: s 101 MET cc_start: 0.8166 (mmm) cc_final: 0.7915 (tmm) REVERT: s 177 MET cc_start: 0.3821 (mmm) cc_final: 0.3575 (mtt) REVERT: t 68 GLN cc_start: 0.6661 (pp30) cc_final: 0.6378 (pp30) REVERT: x 165 LEU cc_start: 0.9281 (mt) cc_final: 0.9018 (mt) REVERT: x 169 LEU cc_start: 0.8761 (mt) cc_final: 0.8405 (mt) REVERT: x 183 ILE cc_start: 0.9323 (mt) cc_final: 0.9078 (mt) REVERT: x 238 ASN cc_start: 0.9216 (p0) cc_final: 0.9012 (p0) REVERT: x 261 PHE cc_start: 0.7904 (m-10) cc_final: 0.7697 (m-80) REVERT: x 369 LEU cc_start: 0.8959 (mp) cc_final: 0.8724 (pp) REVERT: x 389 ASP cc_start: 0.8024 (m-30) cc_final: 0.7629 (m-30) REVERT: y 35 LYS cc_start: 0.9240 (ttmt) cc_final: 0.9023 (tptp) REVERT: y 38 MET cc_start: 0.8622 (ttp) cc_final: 0.8416 (tpp) REVERT: y 65 ILE cc_start: 0.6980 (mm) cc_final: 0.6701 (tp) REVERT: z 76 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5663 (mmt) REVERT: 3 118 PHE cc_start: 0.5560 (m-80) cc_final: 0.4439 (m-80) REVERT: 3 139 MET cc_start: 0.7784 (mtp) cc_final: 0.7409 (mtp) REVERT: 3 141 MET cc_start: 0.5944 (ttp) cc_final: 0.5583 (tmm) REVERT: 4 1 MET cc_start: 0.6041 (tpp) cc_final: 0.5130 (tpp) REVERT: 4 25 TYR cc_start: 0.7945 (t80) cc_final: 0.7738 (t80) REVERT: 5 16 THR cc_start: 0.9252 (m) cc_final: 0.8946 (p) REVERT: 5 21 LEU cc_start: 0.9040 (tt) cc_final: 0.8730 (tt) REVERT: 5 40 ARG cc_start: 0.8406 (ptm-80) cc_final: 0.7863 (ptp90) REVERT: 5 55 ARG cc_start: 0.9300 (ttp80) cc_final: 0.8683 (ttm110) REVERT: 5 177 LEU cc_start: 0.9114 (tt) cc_final: 0.8583 (pp) REVERT: 5 180 TYR cc_start: 0.8526 (m-80) cc_final: 0.7429 (m-80) REVERT: 5 184 ILE cc_start: 0.8618 (pt) cc_final: 0.8280 (pt) REVERT: 5 192 ILE cc_start: 0.8938 (mm) cc_final: 0.8711 (mm) REVERT: 5 198 CYS cc_start: 0.7697 (m) cc_final: 0.7479 (m) REVERT: 5 252 MET cc_start: 0.8025 (tpp) cc_final: 0.7743 (tpp) REVERT: 5 375 LEU cc_start: 0.9411 (tt) cc_final: 0.9087 (mt) REVERT: 5 376 TYR cc_start: 0.8566 (t80) cc_final: 0.7962 (t80) REVERT: 5 473 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: 5 526 TRP cc_start: 0.8129 (p-90) cc_final: 0.7606 (p-90) REVERT: 5 552 ILE cc_start: 0.8416 (mt) cc_final: 0.8142 (mm) outliers start: 33 outliers final: 9 residues processed: 1857 average time/residue: 1.4874 time to fit residues: 4638.9658 Evaluate side-chains 1323 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1312 time to evaluate : 7.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 617 optimal weight: 0.8980 chunk 344 optimal weight: 6.9990 chunk 925 optimal weight: 10.0000 chunk 756 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 1113 optimal weight: 6.9990 chunk 1202 optimal weight: 10.0000 chunk 991 optimal weight: 10.0000 chunk 1104 optimal weight: 0.5980 chunk 379 optimal weight: 8.9990 chunk 893 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 41 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS D 222 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 HIS ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 104 ASN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 GLN N 37 HIS N 91 GLN N 99 GLN N 158 HIS O 5 GLN O 50 ASN ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN Q 188 ASN R 40 GLN R 130 ASN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 HIS ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 91 ASN a 14 HIS ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 ASN a 39 HIS a 60 HIS b 6 ASN e 107 ASN h 98 HIS ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 ASN r 31 ASN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 ASN ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 186 ASN ** x 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 288 ASN ** y 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 12 ASN 5 70 ASN ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 544 ASN ** 5 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 163182 Z= 0.299 Angle : 0.824 19.425 239544 Z= 0.421 Chirality : 0.044 0.293 29845 Planarity : 0.007 0.273 15619 Dihedral : 25.692 179.845 72307 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.05 % Favored : 91.25 % Rotamer: Outliers : 0.22 % Allowed : 5.65 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.48 % 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: -1.80 (0.09), residues: 8147 helix: -0.02 (0.09), residues: 3210 sheet: -1.98 (0.15), residues: 892 loop : -2.01 (0.09), residues: 4045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP x 34 HIS 0.018 0.002 HIS 5 615 PHE 0.046 0.003 PHE e 49 TYR 0.045 0.003 TYR P 130 ARG 0.021 0.001 ARG N 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1643 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1628 time to evaluate : 7.513 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: symmetry clash REVERT: A 196 TRP cc_start: 0.8709 (t60) cc_final: 0.8171 (t60) REVERT: A 209 HIS cc_start: 0.9384 (t-90) cc_final: 0.9096 (t-90) REVERT: A 211 PHE cc_start: 0.8498 (m-10) cc_final: 0.8223 (m-10) REVERT: B 105 VAL cc_start: 0.7694 (t) cc_final: 0.7437 (p) REVERT: B 383 GLU cc_start: 0.8662 (pp20) cc_final: 0.8372 (pm20) REVERT: D 51 MET cc_start: 0.6150 (tmm) cc_final: 0.5818 (tmm) REVERT: D 115 MET cc_start: 0.6833 (mmp) cc_final: 0.6321 (mmm) REVERT: D 157 ASN cc_start: 0.8095 (t0) cc_final: 0.7671 (t0) REVERT: D 239 MET cc_start: 0.3550 (tmm) cc_final: 0.3318 (tmm) REVERT: D 244 HIS cc_start: 0.7053 (m90) cc_final: 0.6702 (m90) REVERT: F 73 MET cc_start: 0.7466 (mtm) cc_final: 0.7020 (mmt) REVERT: F 76 MET cc_start: 0.7383 (ttp) cc_final: 0.6485 (ttp) REVERT: G 101 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8465 (mttp) REVERT: G 234 ARG cc_start: 0.8039 (ttp-170) cc_final: 0.7609 (tpm170) REVERT: G 235 ARG cc_start: 0.7582 (mpt180) cc_final: 0.7286 (mpt180) REVERT: H 92 MET cc_start: 0.4490 (ttm) cc_final: 0.3301 (ttm) REVERT: I 184 MET cc_start: 0.6653 (tpt) cc_final: 0.5643 (tpt) REVERT: J 20 LEU cc_start: 0.7911 (tp) cc_final: 0.7545 (tp) REVERT: L 8 MET cc_start: 0.4810 (mtt) cc_final: 0.3031 (mmt) REVERT: L 90 VAL cc_start: 0.8974 (t) cc_final: 0.8770 (p) REVERT: L 127 PHE cc_start: 0.8785 (t80) cc_final: 0.8578 (t80) REVERT: M 55 MET cc_start: 0.5349 (mmp) cc_final: 0.4896 (ttt) REVERT: N 89 VAL cc_start: 0.7614 (p) cc_final: 0.7377 (p) REVERT: N 105 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6972 (ttm170) REVERT: N 198 LEU cc_start: 0.7669 (tp) cc_final: 0.7372 (tp) REVERT: O 5 GLN cc_start: 0.5039 (OUTLIER) cc_final: 0.3403 (mt0) REVERT: O 118 MET cc_start: 0.7467 (mmp) cc_final: 0.6277 (mmm) REVERT: P 50 ASP cc_start: 0.7804 (m-30) cc_final: 0.7604 (m-30) REVERT: P 80 GLN cc_start: 0.6523 (mm110) cc_final: 0.6200 (mm110) REVERT: P 94 MET cc_start: 0.7389 (tpt) cc_final: 0.6226 (tpt) REVERT: P 130 TYR cc_start: 0.9171 (m-80) cc_final: 0.8764 (m-10) REVERT: Q 16 LYS cc_start: 0.6719 (mmmm) cc_final: 0.6314 (mtpt) REVERT: R 7 GLN cc_start: 0.9165 (mp10) cc_final: 0.8530 (mm-40) REVERT: R 66 ASN cc_start: 0.8387 (m-40) cc_final: 0.8173 (m110) REVERT: R 89 MET cc_start: 0.7812 (tpt) cc_final: 0.7410 (ttm) REVERT: R 95 TRP cc_start: 0.5753 (t-100) cc_final: 0.4972 (t-100) REVERT: R 99 MET cc_start: 0.4732 (mmp) cc_final: 0.4463 (mmm) REVERT: S 157 ARG cc_start: 0.3721 (mmm160) cc_final: 0.3232 (mtm-85) REVERT: T 52 MET cc_start: 0.6652 (mmm) cc_final: 0.6233 (mmm) REVERT: U 85 TYR cc_start: 0.6570 (t80) cc_final: 0.6315 (t80) REVERT: V 36 ASN cc_start: 0.8731 (p0) cc_final: 0.8486 (p0) REVERT: V 90 ARG cc_start: 0.6167 (tpt170) cc_final: 0.5849 (tpp-160) REVERT: V 97 TYR cc_start: 0.6627 (p90) cc_final: 0.6382 (p90) REVERT: X 68 ARG cc_start: 0.8732 (ptm-80) cc_final: 0.8504 (tmm-80) REVERT: X 98 PHE cc_start: 0.7996 (m-80) cc_final: 0.7621 (m-80) REVERT: Y 17 ARG cc_start: 0.9148 (tpm170) cc_final: 0.8944 (tpp-160) REVERT: Y 53 ASP cc_start: 0.7678 (m-30) cc_final: 0.7343 (m-30) REVERT: Y 104 VAL cc_start: 0.7645 (t) cc_final: 0.7323 (t) REVERT: a 58 MET cc_start: 0.4894 (tpt) cc_final: 0.3946 (tpt) REVERT: a 120 GLN cc_start: 0.6835 (tp40) cc_final: 0.6258 (pt0) REVERT: b 57 MET cc_start: 0.1306 (ttm) cc_final: -0.0105 (mmm) REVERT: d 61 ASP cc_start: 0.8935 (t0) cc_final: 0.7915 (p0) REVERT: d 64 ILE cc_start: 0.8559 (mm) cc_final: 0.7816 (tp) REVERT: d 84 ILE cc_start: 0.6495 (mm) cc_final: 0.6131 (mm) REVERT: e 4 LEU cc_start: 0.6310 (mm) cc_final: 0.5787 (tp) REVERT: e 69 MET cc_start: 0.5950 (ttm) cc_final: 0.4864 (mmm) REVERT: g 34 TYR cc_start: 0.8257 (m-80) cc_final: 0.7823 (m-80) REVERT: g 36 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7962 (tptt) REVERT: g 82 MET cc_start: 0.6138 (ttt) cc_final: 0.5553 (ttt) REVERT: h 23 ASP cc_start: 0.7953 (m-30) cc_final: 0.7012 (m-30) REVERT: h 83 LEU cc_start: 0.9056 (mt) cc_final: 0.8482 (mp) REVERT: l 5 LYS cc_start: 0.8819 (mttm) cc_final: 0.8211 (mtmt) REVERT: l 11 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8421 (ttm110) REVERT: l 16 LYS cc_start: 0.9416 (mmtm) cc_final: 0.9068 (mmmm) REVERT: l 18 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8555 (tptp) REVERT: l 19 GLN cc_start: 0.8954 (mt0) cc_final: 0.8584 (mt0) REVERT: n 14 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8122 (mmtt) REVERT: n 22 GLN cc_start: 0.9541 (pp30) cc_final: 0.9312 (pt0) REVERT: o 36 GLN cc_start: 0.8757 (tp40) cc_final: 0.7581 (pp30) REVERT: o 45 GLN cc_start: 0.8478 (pt0) cc_final: 0.7998 (tm-30) REVERT: o 57 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7311 (mtt180) REVERT: p 17 ARG cc_start: 0.8378 (mpp80) cc_final: 0.8169 (mtm180) REVERT: p 49 ARG cc_start: 0.6811 (ttt-90) cc_final: 0.5510 (ptm160) REVERT: p 52 VAL cc_start: 0.7913 (p) cc_final: 0.7109 (p) REVERT: p 79 VAL cc_start: 0.7735 (t) cc_final: 0.7364 (p) REVERT: p 86 LEU cc_start: 0.7106 (mt) cc_final: 0.6831 (mt) REVERT: r 8 MET cc_start: 0.6977 (ttm) cc_final: 0.6122 (ttm) REVERT: r 14 SER cc_start: 0.7992 (p) cc_final: 0.7640 (m) REVERT: s 45 MET cc_start: -0.1075 (mmm) cc_final: -0.1348 (mmp) REVERT: s 101 MET cc_start: 0.8110 (mmm) cc_final: 0.7835 (tmm) REVERT: s 177 MET cc_start: 0.3897 (mmm) cc_final: 0.3586 (mtt) REVERT: x 165 LEU cc_start: 0.9366 (mt) cc_final: 0.8990 (mt) REVERT: x 194 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8335 (mttp) REVERT: x 252 PHE cc_start: 0.8952 (m-10) cc_final: 0.8710 (m-10) REVERT: x 294 GLN cc_start: 0.8640 (mt0) cc_final: 0.8418 (mt0) REVERT: x 399 MET cc_start: 0.7881 (tpt) cc_final: 0.7327 (tpt) REVERT: x 415 ARG cc_start: 0.7923 (ptp90) cc_final: 0.7592 (ptp90) REVERT: y 23 LYS cc_start: 0.8226 (mmpt) cc_final: 0.8002 (mmmt) REVERT: z 76 MET cc_start: 0.6161 (pmm) cc_final: 0.5348 (mmt) REVERT: 3 96 MET cc_start: 0.8298 (ptp) cc_final: 0.7858 (ptp) REVERT: 3 118 PHE cc_start: 0.6040 (m-80) cc_final: 0.4860 (m-10) REVERT: 3 119 LEU cc_start: 0.7823 (mt) cc_final: 0.7363 (mt) REVERT: 3 139 MET cc_start: 0.7863 (mtp) cc_final: 0.7370 (mtp) REVERT: 4 10 PHE cc_start: 0.8924 (t80) cc_final: 0.8599 (t80) REVERT: 5 16 THR cc_start: 0.9384 (m) cc_final: 0.8653 (p) REVERT: 5 55 ARG cc_start: 0.9363 (ttp80) cc_final: 0.8639 (ttm110) REVERT: 5 57 THR cc_start: 0.9626 (m) cc_final: 0.9186 (m) REVERT: 5 133 HIS cc_start: 0.8657 (m90) cc_final: 0.7878 (t-170) REVERT: 5 166 TYR cc_start: 0.6546 (t80) cc_final: 0.5539 (t80) REVERT: 5 176 MET cc_start: 0.8591 (mmm) cc_final: 0.7998 (mmm) REVERT: 5 194 TRP cc_start: 0.7035 (t-100) cc_final: 0.6773 (t-100) REVERT: 5 205 MET cc_start: 0.9357 (tmm) cc_final: 0.8929 (tmm) REVERT: 5 252 MET cc_start: 0.8008 (tpp) cc_final: 0.7695 (tpp) REVERT: 5 370 MET cc_start: 0.7596 (mmp) cc_final: 0.7376 (mmp) REVERT: 5 376 TYR cc_start: 0.8584 (t80) cc_final: 0.8005 (t80) REVERT: 5 390 ILE cc_start: 0.9336 (mt) cc_final: 0.8997 (mt) REVERT: 5 414 MET cc_start: 0.8676 (mmp) cc_final: 0.8405 (mmp) REVERT: 5 428 THR cc_start: 0.8779 (m) cc_final: 0.8560 (p) REVERT: 5 429 TYR cc_start: 0.7680 (m-80) cc_final: 0.7104 (m-10) REVERT: 5 541 LEU cc_start: 0.8539 (mp) cc_final: 0.8199 (mp) REVERT: 5 559 MET cc_start: 0.7654 (tpt) cc_final: 0.7289 (tpt) outliers start: 15 outliers final: 5 residues processed: 1638 average time/residue: 1.3853 time to fit residues: 3821.4807 Evaluate side-chains 1263 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1257 time to evaluate : 7.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 1100 optimal weight: 3.9990 chunk 837 optimal weight: 10.0000 chunk 577 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 531 optimal weight: 20.0000 chunk 747 optimal weight: 40.0000 chunk 1117 optimal weight: 20.0000 chunk 1183 optimal weight: 0.7980 chunk 583 optimal weight: 7.9990 chunk 1059 optimal weight: 0.0020 chunk 318 optimal weight: 8.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- 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 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 119 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 GLN N 178 HIS O 5 GLN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN S 125 GLN U 41 GLN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 HIS Y 56 GLN a 34 ASN b 7 HIS ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 107 ASN ** g 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 HIS m 117 HIS ** o 19 GLN ** 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** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 115 GLN x 127 GLN x 186 ASN ** x 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 288 ASN ** y 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 260 GLN ** 5 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 686 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 163182 Z= 0.195 Angle : 0.717 16.673 239544 Z= 0.363 Chirality : 0.039 0.301 29845 Planarity : 0.006 0.110 15619 Dihedral : 25.505 179.725 72307 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.70 % Favored : 92.64 % Rotamer: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.48 % Twisted General : 0.10 % 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: 8147 helix: 0.29 (0.09), residues: 3220 sheet: -1.70 (0.16), residues: 883 loop : -1.78 (0.09), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP x 34 HIS 0.018 0.001 HIS 5 615 PHE 0.029 0.002 PHE x 156 TYR 0.031 0.002 TYR F 53 ARG 0.014 0.001 ARG N 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1599 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1589 time to evaluate : 8.846 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: A 8 GLN cc_start: 0.8022 (tt0) cc_final: 0.7761 (tt0) REVERT: A 158 ILE cc_start: 0.8716 (mp) cc_final: 0.8322 (mm) REVERT: A 196 TRP cc_start: 0.8367 (t60) cc_final: 0.8153 (t60) REVERT: A 204 MET cc_start: 0.9107 (mtm) cc_final: 0.8774 (mtm) REVERT: A 211 PHE cc_start: 0.8216 (m-10) cc_final: 0.7861 (m-10) REVERT: A 217 GLN cc_start: 0.7334 (mt0) cc_final: 0.6920 (pt0) REVERT: B 383 GLU cc_start: 0.8739 (pp20) cc_final: 0.8528 (pm20) REVERT: C 65 GLU cc_start: 0.9336 (tp30) cc_final: 0.9107 (tp30) REVERT: C 66 SER cc_start: 0.9259 (t) cc_final: 0.8991 (t) REVERT: C 101 MET cc_start: 0.5838 (ptm) cc_final: 0.5075 (tpt) REVERT: C 169 LEU cc_start: 0.9212 (tp) cc_final: 0.8955 (tp) REVERT: C 200 ARG cc_start: 0.7474 (ttm170) cc_final: 0.5846 (ptp90) REVERT: C 209 VAL cc_start: 0.7234 (t) cc_final: 0.6802 (t) REVERT: C 284 MET cc_start: 0.7335 (tmm) cc_final: 0.6952 (tmm) REVERT: D 115 MET cc_start: 0.6803 (mmp) cc_final: 0.6199 (mmm) REVERT: D 157 ASN cc_start: 0.7775 (t0) cc_final: 0.7355 (t0) REVERT: D 235 MET cc_start: 0.4411 (ptm) cc_final: 0.3885 (ptm) REVERT: D 239 MET cc_start: 0.3386 (tmm) cc_final: 0.3087 (tmm) REVERT: D 244 HIS cc_start: 0.6791 (m90) cc_final: 0.6202 (m-70) REVERT: F 76 MET cc_start: 0.7244 (ttp) cc_final: 0.6435 (tmm) REVERT: F 93 PHE cc_start: 0.3918 (t80) cc_final: 0.3666 (t80) REVERT: G 51 LEU cc_start: 0.0395 (OUTLIER) cc_final: 0.0071 (tt) REVERT: H 55 LEU cc_start: 0.3619 (tp) cc_final: 0.3084 (pp) REVERT: H 92 MET cc_start: 0.4017 (ttm) cc_final: 0.2739 (ttm) REVERT: I 92 HIS cc_start: 0.4134 (m-70) cc_final: 0.3197 (m170) REVERT: I 182 GLU cc_start: 0.7997 (pm20) cc_final: 0.7744 (pm20) REVERT: J 20 LEU cc_start: 0.7505 (tp) cc_final: 0.7303 (tp) REVERT: L 8 MET cc_start: 0.4552 (mtt) cc_final: 0.2414 (mmt) REVERT: L 90 VAL cc_start: 0.8858 (t) cc_final: 0.8635 (p) REVERT: M 118 MET cc_start: 0.7805 (mmm) cc_final: 0.7594 (tpt) REVERT: N 198 LEU cc_start: 0.7712 (tp) cc_final: 0.7330 (tp) REVERT: O 5 GLN cc_start: 0.5149 (OUTLIER) cc_final: 0.3266 (mt0) REVERT: O 92 THR cc_start: 0.5864 (t) cc_final: 0.5663 (t) REVERT: O 118 MET cc_start: 0.7297 (mmp) cc_final: 0.6174 (mmm) REVERT: P 18 ARG cc_start: 0.5935 (ttp80) cc_final: 0.5581 (ttp80) REVERT: P 80 GLN cc_start: 0.6442 (mm110) cc_final: 0.6142 (mm110) REVERT: P 94 MET cc_start: 0.7121 (tpt) cc_final: 0.6789 (tpt) REVERT: P 130 TYR cc_start: 0.9064 (m-80) cc_final: 0.8783 (m-10) REVERT: Q 4 ASP cc_start: 0.7415 (t0) cc_final: 0.7097 (p0) REVERT: Q 16 LYS cc_start: 0.6601 (mmmm) cc_final: 0.6384 (ttmt) REVERT: Q 27 LEU cc_start: 0.6971 (tp) cc_final: 0.6681 (pp) REVERT: R 7 GLN cc_start: 0.9151 (mp10) cc_final: 0.8459 (mm-40) REVERT: R 47 ASP cc_start: 0.9208 (t0) cc_final: 0.9002 (t0) REVERT: R 66 ASN cc_start: 0.8124 (m-40) cc_final: 0.7770 (m110) REVERT: R 75 HIS cc_start: 0.7713 (m90) cc_final: 0.6881 (m90) REVERT: R 89 MET cc_start: 0.7698 (tpt) cc_final: 0.7209 (ttm) REVERT: R 95 TRP cc_start: 0.5694 (t-100) cc_final: 0.5279 (t-100) REVERT: S 41 LYS cc_start: 0.7859 (tmtt) cc_final: 0.7656 (tmtt) REVERT: S 93 MET cc_start: 0.7229 (tmm) cc_final: 0.6876 (tmm) REVERT: T 52 MET cc_start: 0.6590 (mmm) cc_final: 0.6168 (mmm) REVERT: U 41 GLN cc_start: 0.8348 (pt0) cc_final: 0.8070 (pp30) REVERT: V 27 ASN cc_start: 0.8371 (p0) cc_final: 0.7450 (t0) REVERT: V 36 ASN cc_start: 0.8729 (p0) cc_final: 0.8512 (p0) REVERT: V 60 MET cc_start: 0.6359 (tmm) cc_final: 0.6126 (ptm) REVERT: V 97 TYR cc_start: 0.6638 (p90) cc_final: 0.6196 (p90) REVERT: V 105 ILE cc_start: 0.8918 (mp) cc_final: 0.8606 (mp) REVERT: W 23 ARG cc_start: 0.7228 (mmm-85) cc_final: 0.6907 (mmm-85) REVERT: X 56 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7270 (mmm-85) REVERT: X 62 ARG cc_start: 0.7071 (mmp80) cc_final: 0.6627 (mmp80) REVERT: X 98 PHE cc_start: 0.7894 (m-80) cc_final: 0.7447 (m-80) REVERT: X 101 ASP cc_start: 0.7652 (t0) cc_final: 0.7440 (t70) REVERT: X 103 LYS cc_start: 0.8402 (mttt) cc_final: 0.8009 (mttt) REVERT: Y 104 VAL cc_start: 0.8224 (t) cc_final: 0.7999 (t) REVERT: a 58 MET cc_start: 0.4454 (tpt) cc_final: 0.4006 (tpt) REVERT: a 120 GLN cc_start: 0.6929 (tp40) cc_final: 0.6174 (pt0) REVERT: b 57 MET cc_start: 0.0758 (ttm) cc_final: -0.0239 (mmm) REVERT: c 22 MET cc_start: 0.6728 (mmp) cc_final: 0.6177 (tpt) REVERT: d 51 LYS cc_start: 0.8813 (tppt) cc_final: 0.8417 (ptpp) REVERT: d 61 ASP cc_start: 0.8759 (t0) cc_final: 0.7644 (p0) REVERT: d 64 ILE cc_start: 0.8371 (mm) cc_final: 0.7799 (tp) REVERT: d 93 ASN cc_start: 0.4989 (t0) cc_final: 0.4221 (t0) REVERT: d 96 GLU cc_start: 0.7633 (tp30) cc_final: 0.7404 (tt0) REVERT: e 4 LEU cc_start: 0.6669 (mm) cc_final: 0.6069 (tp) REVERT: e 69 MET cc_start: 0.5651 (ttm) cc_final: 0.4795 (mmm) REVERT: f 51 TYR cc_start: 0.6181 (p90) cc_final: 0.5799 (p90) REVERT: g 34 TYR cc_start: 0.8058 (m-80) cc_final: 0.7774 (m-80) REVERT: g 36 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7938 (tptt) REVERT: g 82 MET cc_start: 0.6007 (ttt) cc_final: 0.5358 (mtp) REVERT: h 23 ASP cc_start: 0.7902 (m-30) cc_final: 0.7007 (m-30) REVERT: h 25 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7946 (mmtt) REVERT: h 83 LEU cc_start: 0.8792 (mt) cc_final: 0.8306 (mt) REVERT: l 5 LYS cc_start: 0.8802 (mttm) cc_final: 0.8268 (mtmt) REVERT: l 48 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8530 (mmmt) REVERT: n 14 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7926 (mmtt) REVERT: n 22 GLN cc_start: 0.9565 (pp30) cc_final: 0.9318 (pt0) REVERT: o 17 LYS cc_start: 0.9031 (ptpp) cc_final: 0.8803 (mmtt) REVERT: o 36 GLN cc_start: 0.8661 (tp40) cc_final: 0.7492 (pp30) REVERT: o 96 ASP cc_start: 0.7512 (m-30) cc_final: 0.7265 (m-30) REVERT: p 49 ARG cc_start: 0.6904 (ttt-90) cc_final: 0.5526 (ptm-80) REVERT: p 52 VAL cc_start: 0.7656 (p) cc_final: 0.7119 (p) REVERT: p 61 MET cc_start: 0.7878 (mpp) cc_final: 0.7643 (mpp) REVERT: p 79 VAL cc_start: 0.7638 (t) cc_final: 0.7335 (p) REVERT: p 86 LEU cc_start: 0.7215 (mt) cc_final: 0.6911 (mt) REVERT: r 8 MET cc_start: 0.7045 (ttm) cc_final: 0.6393 (ttm) REVERT: s 177 MET cc_start: 0.3937 (mmm) cc_final: 0.3636 (mtt) REVERT: x 165 LEU cc_start: 0.9391 (mt) cc_final: 0.8873 (pp) REVERT: x 182 PHE cc_start: 0.7797 (m-10) cc_final: 0.7541 (m-10) REVERT: x 183 ILE cc_start: 0.9075 (mm) cc_final: 0.8746 (mm) REVERT: x 194 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8397 (mtmm) REVERT: x 276 TYR cc_start: 0.7766 (m-80) cc_final: 0.7503 (m-80) REVERT: x 294 GLN cc_start: 0.8874 (mt0) cc_final: 0.8556 (mt0) REVERT: x 457 TYR cc_start: 0.8118 (t80) cc_final: 0.7747 (t80) REVERT: y 23 LYS cc_start: 0.8236 (mmpt) cc_final: 0.7909 (mmmt) REVERT: y 38 MET cc_start: 0.9118 (tpp) cc_final: 0.8834 (mtt) REVERT: z 76 MET cc_start: 0.6109 (pmm) cc_final: 0.5393 (mmt) REVERT: 3 96 MET cc_start: 0.8241 (ptp) cc_final: 0.7972 (ptt) REVERT: 3 118 PHE cc_start: 0.5838 (m-80) cc_final: 0.4528 (m-80) REVERT: 3 119 LEU cc_start: 0.7319 (mt) cc_final: 0.6974 (mt) REVERT: 3 139 MET cc_start: 0.7757 (mtp) cc_final: 0.7012 (mtp) REVERT: 3 140 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7547 (mmm160) REVERT: 3 143 LEU cc_start: 0.8720 (mp) cc_final: 0.8494 (mp) REVERT: 4 10 PHE cc_start: 0.8955 (t80) cc_final: 0.8665 (t80) REVERT: 5 55 ARG cc_start: 0.9370 (ttp80) cc_final: 0.9020 (ptm-80) REVERT: 5 57 THR cc_start: 0.9421 (m) cc_final: 0.9196 (m) REVERT: 5 133 HIS cc_start: 0.8727 (m90) cc_final: 0.7980 (t-170) REVERT: 5 176 MET cc_start: 0.8184 (mmm) cc_final: 0.6091 (mmm) REVERT: 5 177 LEU cc_start: 0.9335 (tp) cc_final: 0.8984 (tp) REVERT: 5 180 TYR cc_start: 0.8164 (m-80) cc_final: 0.7354 (m-80) REVERT: 5 205 MET cc_start: 0.9218 (tmm) cc_final: 0.8776 (tmm) REVERT: 5 252 MET cc_start: 0.7887 (tpp) cc_final: 0.7597 (tpp) REVERT: 5 349 VAL cc_start: 0.8790 (p) cc_final: 0.8242 (p) REVERT: 5 366 LEU cc_start: 0.9234 (tt) cc_final: 0.8355 (tt) REVERT: 5 429 TYR cc_start: 0.7415 (m-80) cc_final: 0.7151 (m-10) REVERT: 5 501 ILE cc_start: 0.8997 (pt) cc_final: 0.8715 (mp) REVERT: 5 541 LEU cc_start: 0.8314 (mp) cc_final: 0.7975 (mp) REVERT: 5 559 MET cc_start: 0.7664 (tpt) cc_final: 0.7342 (tpt) outliers start: 10 outliers final: 1 residues processed: 1596 average time/residue: 1.3337 time to fit residues: 3591.1312 Evaluate side-chains 1231 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1228 time to evaluate : 6.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 985 optimal weight: 20.0000 chunk 671 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 880 optimal weight: 10.0000 chunk 488 optimal weight: 4.9990 chunk 1009 optimal weight: 20.0000 chunk 817 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 604 optimal weight: 10.0000 chunk 1061 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN B 376 HIS C 38 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 246 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN O 5 GLN P 54 GLN P 80 GLN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 GLN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 HIS W 50 ASN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 7 HIS c 72 HIS ** g 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 HIS ** m 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 109 ASN ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 ASN ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 154 GLN ** x 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 275 GLN x 277 ASN x 288 ASN x 398 GLN ** 5 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 514 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 163182 Z= 0.342 Angle : 0.845 21.198 239544 Z= 0.425 Chirality : 0.044 0.340 29845 Planarity : 0.007 0.113 15619 Dihedral : 25.629 179.995 72307 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 31.18 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.51 % Favored : 90.88 % Rotamer: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.48 % 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: -1.66 (0.09), residues: 8147 helix: -0.04 (0.09), residues: 3239 sheet: -1.61 (0.16), residues: 908 loop : -1.89 (0.09), residues: 4000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP x 34 HIS 0.021 0.002 HIS I 130 PHE 0.041 0.003 PHE x 156 TYR 0.041 0.003 TYR D 207 ARG 0.030 0.001 ARG i 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1470 time to evaluate : 6.803 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: A 8 GLN cc_start: 0.8296 (tt0) cc_final: 0.8071 (tt0) REVERT: A 158 ILE cc_start: 0.8713 (mp) cc_final: 0.8313 (mm) REVERT: A 162 ASN cc_start: 0.5961 (OUTLIER) cc_final: 0.5677 (p0) REVERT: A 196 TRP cc_start: 0.8750 (t60) cc_final: 0.8188 (t60) REVERT: A 204 MET cc_start: 0.9286 (mtm) cc_final: 0.8823 (mtm) REVERT: A 217 GLN cc_start: 0.7513 (mt0) cc_final: 0.7155 (pt0) REVERT: A 241 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7274 (mtt-85) REVERT: B 153 MET cc_start: 0.7983 (ttt) cc_final: 0.7592 (ttp) REVERT: B 168 MET cc_start: 0.6207 (ttm) cc_final: 0.5729 (ttm) REVERT: C 65 GLU cc_start: 0.9415 (tp30) cc_final: 0.9108 (tp30) REVERT: C 169 LEU cc_start: 0.9187 (tp) cc_final: 0.8942 (pp) REVERT: C 200 ARG cc_start: 0.7723 (ttm170) cc_final: 0.6179 (ptp90) REVERT: D 51 MET cc_start: 0.6088 (tmm) cc_final: 0.5873 (tmm) REVERT: D 115 MET cc_start: 0.7206 (mmp) cc_final: 0.6376 (mmm) REVERT: D 235 MET cc_start: 0.4847 (ptm) cc_final: 0.4530 (ptm) REVERT: F 43 MET cc_start: 0.5188 (mtm) cc_final: 0.4934 (mtm) REVERT: F 76 MET cc_start: 0.7470 (ttp) cc_final: 0.6609 (ttp) REVERT: H 55 LEU cc_start: 0.3241 (tp) cc_final: 0.2690 (pp) REVERT: H 92 MET cc_start: 0.3788 (ttm) cc_final: 0.2995 (ttm) REVERT: H 120 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5708 (tp30) REVERT: I 73 ASN cc_start: 0.6968 (t0) cc_final: 0.6461 (m-40) REVERT: I 182 GLU cc_start: 0.8003 (pm20) cc_final: 0.7502 (pm20) REVERT: J 20 LEU cc_start: 0.7739 (tp) cc_final: 0.7409 (tp) REVERT: L 8 MET cc_start: 0.4499 (mtt) cc_final: 0.3268 (mtp) REVERT: L 25 TRP cc_start: 0.6756 (m100) cc_final: 0.6384 (m100) REVERT: N 99 GLN cc_start: 0.8112 (tt0) cc_final: 0.7548 (tt0) REVERT: N 105 ARG cc_start: 0.7328 (ttm170) cc_final: 0.6875 (ttm170) REVERT: O 5 GLN cc_start: 0.5507 (OUTLIER) cc_final: 0.3587 (mt0) REVERT: O 118 MET cc_start: 0.7284 (mmp) cc_final: 0.6340 (mmm) REVERT: P 50 ASP cc_start: 0.7756 (m-30) cc_final: 0.7543 (m-30) REVERT: P 126 ARG cc_start: 0.8903 (ttm110) cc_final: 0.8339 (ptp-110) REVERT: P 149 ILE cc_start: 0.6416 (mm) cc_final: 0.6045 (mm) REVERT: R 7 GLN cc_start: 0.9135 (mp10) cc_final: 0.8575 (mm-40) REVERT: R 66 ASN cc_start: 0.7913 (m-40) cc_final: 0.7571 (m110) REVERT: R 70 ARG cc_start: 0.5948 (tpt170) cc_final: 0.5669 (tpt170) REVERT: R 80 LYS cc_start: 0.7818 (mmpt) cc_final: 0.7526 (mmmt) REVERT: R 89 MET cc_start: 0.7948 (tpt) cc_final: 0.7390 (ttm) REVERT: R 99 MET cc_start: 0.5474 (mmp) cc_final: 0.4964 (mmt) REVERT: S 12 VAL cc_start: 0.8399 (m) cc_final: 0.8026 (t) REVERT: S 93 MET cc_start: 0.7444 (tmm) cc_final: 0.6538 (tmm) REVERT: T 81 LYS cc_start: 0.4271 (pttt) cc_final: 0.3577 (pttt) REVERT: U 42 PHE cc_start: 0.7805 (t80) cc_final: 0.7416 (t80) REVERT: U 90 TYR cc_start: 0.8093 (t80) cc_final: 0.7801 (t80) REVERT: V 60 MET cc_start: 0.6547 (tmm) cc_final: 0.6321 (tmm) REVERT: X 62 ARG cc_start: 0.6989 (mmp80) cc_final: 0.6293 (mmp80) REVERT: X 71 LEU cc_start: 0.8233 (tt) cc_final: 0.8016 (mm) REVERT: X 92 ASP cc_start: 0.8570 (t0) cc_final: 0.8283 (t0) REVERT: X 103 LYS cc_start: 0.8589 (mttt) cc_final: 0.8120 (mttt) REVERT: Y 38 LEU cc_start: 0.8461 (mt) cc_final: 0.7972 (mt) REVERT: Z 70 SER cc_start: 0.7993 (m) cc_final: 0.7782 (m) REVERT: a 78 LEU cc_start: 0.6741 (mt) cc_final: 0.6294 (mt) REVERT: a 81 LEU cc_start: 0.7130 (mt) cc_final: 0.6667 (mt) REVERT: a 112 LEU cc_start: 0.9094 (mt) cc_final: 0.8703 (mp) REVERT: a 120 GLN cc_start: 0.7317 (tp40) cc_final: 0.6071 (pt0) REVERT: b 57 MET cc_start: 0.0731 (ttm) cc_final: -0.0198 (mmm) REVERT: c 22 MET cc_start: 0.6774 (mmp) cc_final: 0.6026 (tpt) REVERT: d 51 LYS cc_start: 0.8846 (tppt) cc_final: 0.8592 (ptmm) REVERT: d 61 ASP cc_start: 0.8722 (t0) cc_final: 0.7551 (p0) REVERT: d 64 ILE cc_start: 0.8616 (mm) cc_final: 0.7803 (tp) REVERT: e 4 LEU cc_start: 0.6789 (mm) cc_final: 0.6433 (mm) REVERT: e 23 HIS cc_start: 0.6435 (t70) cc_final: 0.6148 (t70) REVERT: e 57 ASN cc_start: 0.6987 (m-40) cc_final: 0.6683 (p0) REVERT: e 69 MET cc_start: 0.5879 (ttm) cc_final: 0.5330 (mmm) REVERT: g 34 TYR cc_start: 0.8119 (m-80) cc_final: 0.7729 (m-80) REVERT: g 82 MET cc_start: 0.6101 (ttt) cc_final: 0.5480 (mtp) REVERT: h 23 ASP cc_start: 0.8016 (m-30) cc_final: 0.7218 (m-30) REVERT: h 25 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8085 (mmtt) REVERT: h 44 LEU cc_start: 0.9222 (mt) cc_final: 0.8878 (mt) REVERT: h 83 LEU cc_start: 0.8966 (mt) cc_final: 0.8524 (mt) REVERT: l 5 LYS cc_start: 0.8882 (mttm) cc_final: 0.8329 (mtmt) REVERT: l 48 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8475 (mmmt) REVERT: m 78 ILE cc_start: 0.6082 (tp) cc_final: 0.5823 (tp) REVERT: n 14 LYS cc_start: 0.8288 (mtpt) cc_final: 0.8017 (mmtt) REVERT: o 17 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8647 (mmtt) REVERT: o 52 THR cc_start: 0.8285 (p) cc_final: 0.7941 (p) REVERT: o 92 GLU cc_start: 0.7307 (tp30) cc_final: 0.6428 (pm20) REVERT: p 17 ARG cc_start: 0.8360 (mpp80) cc_final: 0.7874 (mtp180) REVERT: p 47 MET cc_start: 0.6480 (tpt) cc_final: 0.4695 (tpt) REVERT: p 49 ARG cc_start: 0.7355 (ttt-90) cc_final: 0.5611 (ppt170) REVERT: p 79 VAL cc_start: 0.7781 (t) cc_final: 0.7465 (p) REVERT: p 86 LEU cc_start: 0.7061 (mt) cc_final: 0.6801 (mt) REVERT: r 8 MET cc_start: 0.7134 (ttm) cc_final: 0.6083 (ttm) REVERT: r 113 ARG cc_start: 0.5947 (mmt180) cc_final: 0.5278 (mmm160) REVERT: s 45 MET cc_start: -0.0711 (mmp) cc_final: -0.1160 (mmt) REVERT: s 60 MET cc_start: 0.2344 (mtp) cc_final: 0.1673 (mmm) REVERT: s 177 MET cc_start: 0.3847 (mmm) cc_final: 0.3565 (mtt) REVERT: x 65 MET cc_start: 0.8332 (ptm) cc_final: 0.8037 (ptm) REVERT: x 98 LYS cc_start: 0.7397 (mptt) cc_final: 0.7177 (mmtm) REVERT: x 121 MET cc_start: 0.8293 (tpt) cc_final: 0.7920 (tpp) REVERT: x 161 ILE cc_start: 0.7535 (mm) cc_final: 0.7198 (mm) REVERT: x 165 LEU cc_start: 0.9401 (mt) cc_final: 0.9068 (mt) REVERT: x 171 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7509 (ttpp) REVERT: x 179 ILE cc_start: 0.8321 (mt) cc_final: 0.8028 (mt) REVERT: x 183 ILE cc_start: 0.8949 (mm) cc_final: 0.8688 (mm) REVERT: x 194 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8476 (mtmt) REVERT: x 275 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7136 (pp30) REVERT: x 294 GLN cc_start: 0.8788 (mt0) cc_final: 0.8473 (mt0) REVERT: x 389 ASP cc_start: 0.8395 (m-30) cc_final: 0.8048 (m-30) REVERT: x 399 MET cc_start: 0.8098 (tpt) cc_final: 0.6498 (tpt) REVERT: y 23 LYS cc_start: 0.8412 (mmpt) cc_final: 0.8210 (mmmt) REVERT: y 38 MET cc_start: 0.9087 (tpp) cc_final: 0.8764 (mtt) REVERT: z 76 MET cc_start: 0.6200 (pmm) cc_final: 0.5341 (mmt) REVERT: 3 118 PHE cc_start: 0.6265 (m-80) cc_final: 0.4853 (m-10) REVERT: 3 139 MET cc_start: 0.7969 (mtp) cc_final: 0.7412 (mtp) REVERT: 5 55 ARG cc_start: 0.9392 (ttp80) cc_final: 0.9025 (ptm-80) REVERT: 5 94 ILE cc_start: 0.9457 (mm) cc_final: 0.9225 (tp) REVERT: 5 133 HIS cc_start: 0.8691 (m90) cc_final: 0.8115 (t-170) REVERT: 5 349 VAL cc_start: 0.8865 (p) cc_final: 0.8239 (p) REVERT: 5 367 LEU cc_start: 0.9544 (mm) cc_final: 0.9116 (mm) REVERT: 5 370 MET cc_start: 0.7351 (mmp) cc_final: 0.6962 (mmp) REVERT: 5 379 PHE cc_start: 0.8953 (m-10) cc_final: 0.8516 (t80) REVERT: 5 414 MET cc_start: 0.8612 (mmp) cc_final: 0.8193 (mmp) REVERT: 5 430 MET cc_start: 0.8402 (ttt) cc_final: 0.7987 (tmm) REVERT: 5 431 LYS cc_start: 0.8725 (tppt) cc_final: 0.8451 (tppt) REVERT: 5 467 PHE cc_start: 0.8677 (t80) cc_final: 0.8095 (t80) REVERT: 5 523 MET cc_start: 0.7061 (ppp) cc_final: 0.6838 (ppp) REVERT: 5 526 TRP cc_start: 0.8494 (p-90) cc_final: 0.8257 (p-90) outliers start: 6 outliers final: 0 residues processed: 1475 average time/residue: 1.2903 time to fit residues: 3214.7718 Evaluate side-chains 1146 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1143 time to evaluate : 6.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 398 optimal weight: 20.0000 chunk 1065 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 694 optimal weight: 9.9990 chunk 292 optimal weight: 7.9990 chunk 1184 optimal weight: 0.0980 chunk 983 optimal weight: 4.9990 chunk 548 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 391 optimal weight: 4.9990 chunk 621 optimal weight: 10.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN A 217 GLN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 GLN ** N 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN O 5 GLN O 65 ASN O 150 GLN ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 HIS ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 HIS W 17 HIS X 105 ASN Y 20 ASN ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 ASN i 26 HIS m 117 HIS ** o 19 GLN ** 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 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 47 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 411 HIS ** z 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 163182 Z= 0.245 Angle : 0.750 20.395 239544 Z= 0.377 Chirality : 0.041 0.322 29845 Planarity : 0.006 0.116 15619 Dihedral : 25.617 179.880 72307 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.49 % Favored : 91.89 % Rotamer: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.48 % 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: -1.47 (0.09), residues: 8147 helix: 0.17 (0.09), residues: 3199 sheet: -1.47 (0.16), residues: 923 loop : -1.82 (0.09), residues: 4025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 252 HIS 0.019 0.002 HIS j 76 PHE 0.049 0.002 PHE J 107 TYR 0.033 0.002 TYR x 455 ARG 0.018 0.001 ARG x 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1452 time to evaluate : 6.797 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: A 3 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8490 (ttp80) REVERT: A 16 PHE cc_start: 0.8415 (m-80) cc_final: 0.7646 (m-80) REVERT: A 158 ILE cc_start: 0.8803 (mp) cc_final: 0.8398 (mm) REVERT: A 162 ASN cc_start: 0.5304 (p0) cc_final: 0.5010 (p0) REVERT: A 196 TRP cc_start: 0.8580 (t60) cc_final: 0.8040 (t60) REVERT: A 198 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6600 (tpt170) REVERT: A 204 MET cc_start: 0.9308 (mtm) cc_final: 0.8885 (mtm) REVERT: A 217 GLN cc_start: 0.7192 (mt0) cc_final: 0.6772 (pt0) REVERT: A 241 ARG cc_start: 0.7475 (mtt-85) cc_final: 0.7221 (mtt-85) REVERT: B 168 MET cc_start: 0.6824 (ttm) cc_final: 0.6442 (ttm) REVERT: B 336 CYS cc_start: 0.5982 (m) cc_final: 0.5561 (m) REVERT: B 383 GLU cc_start: 0.8795 (pp20) cc_final: 0.8518 (pm20) REVERT: B 389 MET cc_start: 0.7587 (tpt) cc_final: 0.7248 (tpp) REVERT: C 65 GLU cc_start: 0.9441 (tp30) cc_final: 0.9192 (tp30) REVERT: C 66 SER cc_start: 0.9214 (t) cc_final: 0.8796 (t) REVERT: C 169 LEU cc_start: 0.9071 (tp) cc_final: 0.8867 (pp) REVERT: C 200 ARG cc_start: 0.7746 (ttm170) cc_final: 0.6253 (ptp90) REVERT: D 115 MET cc_start: 0.6926 (mmp) cc_final: 0.6487 (mmm) REVERT: E 112 TYR cc_start: 0.4427 (m-80) cc_final: 0.4207 (m-80) REVERT: F 43 MET cc_start: 0.5036 (mtm) cc_final: 0.4820 (mtm) REVERT: F 76 MET cc_start: 0.7101 (ttp) cc_final: 0.6734 (ttp) REVERT: F 192 LEU cc_start: 0.8633 (mt) cc_final: 0.8207 (tp) REVERT: H 55 LEU cc_start: 0.3615 (tp) cc_final: 0.3069 (pp) REVERT: H 92 MET cc_start: 0.4125 (ttm) cc_final: 0.3689 (ttm) REVERT: I 73 ASN cc_start: 0.7086 (t0) cc_final: 0.6782 (m-40) REVERT: I 182 GLU cc_start: 0.7972 (pm20) cc_final: 0.7453 (pm20) REVERT: J 12 MET cc_start: -0.2299 (ttt) cc_final: -0.2597 (tpp) REVERT: J 20 LEU cc_start: 0.7833 (tp) cc_final: 0.7582 (tp) REVERT: L 8 MET cc_start: 0.4447 (mtt) cc_final: 0.2853 (mtp) REVERT: L 25 TRP cc_start: 0.6672 (m100) cc_final: 0.6189 (m100) REVERT: L 33 ILE cc_start: 0.8043 (mm) cc_final: 0.7339 (mm) REVERT: L 37 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7712 (mmtp) REVERT: L 184 MET cc_start: 0.6915 (mmp) cc_final: 0.6714 (ptm) REVERT: M 118 MET cc_start: 0.7793 (mmp) cc_final: 0.6813 (mmp) REVERT: N 14 LYS cc_start: 0.7245 (ttpt) cc_final: 0.6969 (ttpt) REVERT: N 99 GLN cc_start: 0.7589 (tt0) cc_final: 0.7271 (tt0) REVERT: N 105 ARG cc_start: 0.7474 (ttm170) cc_final: 0.7064 (ttm170) REVERT: O 5 GLN cc_start: 0.5501 (OUTLIER) cc_final: 0.3292 (mt0) REVERT: O 118 MET cc_start: 0.7443 (mmp) cc_final: 0.6531 (mmm) REVERT: P 86 LYS cc_start: 0.8478 (tppt) cc_final: 0.8011 (tppt) REVERT: P 125 MET cc_start: 0.8229 (mmp) cc_final: 0.8017 (mmp) REVERT: Q 4 ASP cc_start: 0.7605 (p0) cc_final: 0.7250 (p0) REVERT: Q 26 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.7177 (mtt-85) REVERT: R 7 GLN cc_start: 0.9099 (mp10) cc_final: 0.8486 (mm-40) REVERT: R 31 GLU cc_start: 0.8330 (mp0) cc_final: 0.7763 (mm-30) REVERT: R 45 ILE cc_start: 0.8694 (mm) cc_final: 0.8378 (tp) REVERT: R 47 ASP cc_start: 0.9231 (t0) cc_final: 0.9030 (t0) REVERT: R 66 ASN cc_start: 0.7782 (m-40) cc_final: 0.7509 (m110) REVERT: R 70 ARG cc_start: 0.5356 (tpt170) cc_final: 0.5122 (tpt170) REVERT: R 75 HIS cc_start: 0.7585 (m90) cc_final: 0.6822 (m170) REVERT: R 80 LYS cc_start: 0.7768 (mmpt) cc_final: 0.7473 (mmmt) REVERT: R 89 MET cc_start: 0.7746 (tpt) cc_final: 0.7204 (ttm) REVERT: R 99 MET cc_start: 0.5134 (mmp) cc_final: 0.4366 (mmt) REVERT: S 93 MET cc_start: 0.7448 (tmm) cc_final: 0.6560 (tmm) REVERT: T 45 MET cc_start: 0.7195 (ttm) cc_final: 0.6895 (mtm) REVERT: T 65 TYR cc_start: 0.7874 (p90) cc_final: 0.7343 (p90) REVERT: T 74 ILE cc_start: 0.5603 (tt) cc_final: 0.5067 (tt) REVERT: T 81 LYS cc_start: 0.4226 (pttt) cc_final: 0.3587 (pttt) REVERT: U 42 PHE cc_start: 0.7839 (t80) cc_final: 0.7632 (t80) REVERT: U 46 ARG cc_start: 0.7152 (mmp80) cc_final: 0.6907 (mmp80) REVERT: U 75 GLU cc_start: 0.7685 (mp0) cc_final: 0.7154 (pm20) REVERT: U 85 TYR cc_start: 0.6680 (t80) cc_final: 0.6258 (t80) REVERT: U 94 ASN cc_start: 0.8731 (m-40) cc_final: 0.8355 (t0) REVERT: U 96 LEU cc_start: 0.7523 (mt) cc_final: 0.7262 (mt) REVERT: V 39 ILE cc_start: 0.9247 (mp) cc_final: 0.9009 (mp) REVERT: V 74 LYS cc_start: 0.9383 (mppt) cc_final: 0.9044 (mmmt) REVERT: W 21 TYR cc_start: 0.5697 (t80) cc_final: 0.5141 (t80) REVERT: W 23 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7125 (mmm-85) REVERT: X 56 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7636 (mmt180) REVERT: X 68 ARG cc_start: 0.8635 (tmm-80) cc_final: 0.8423 (tmm-80) REVERT: X 79 PHE cc_start: 0.7784 (p90) cc_final: 0.7402 (p90) REVERT: X 101 ASP cc_start: 0.8085 (t0) cc_final: 0.7853 (t0) REVERT: Z 116 VAL cc_start: 0.8761 (t) cc_final: 0.8495 (p) REVERT: a 78 LEU cc_start: 0.6564 (mt) cc_final: 0.5968 (mt) REVERT: a 81 LEU cc_start: 0.6957 (mt) cc_final: 0.6628 (mt) REVERT: a 112 LEU cc_start: 0.9072 (mt) cc_final: 0.8675 (mp) REVERT: a 120 GLN cc_start: 0.7334 (tp40) cc_final: 0.6047 (pt0) REVERT: b 57 MET cc_start: 0.0735 (ttm) cc_final: -0.0345 (mmm) REVERT: c 22 MET cc_start: 0.6923 (mmp) cc_final: 0.6148 (tpt) REVERT: d 51 LYS cc_start: 0.8883 (tppt) cc_final: 0.8628 (ptmm) REVERT: d 61 ASP cc_start: 0.8309 (t0) cc_final: 0.7246 (p0) REVERT: d 64 ILE cc_start: 0.8717 (mm) cc_final: 0.7933 (tp) REVERT: e 23 HIS cc_start: 0.6357 (t70) cc_final: 0.6115 (t70) REVERT: e 48 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7615 (mtm180) REVERT: e 69 MET cc_start: 0.5975 (ttm) cc_final: 0.5259 (mmt) REVERT: g 34 TYR cc_start: 0.8116 (m-80) cc_final: 0.7792 (m-80) REVERT: g 82 MET cc_start: 0.6158 (ttt) cc_final: 0.5693 (mtp) REVERT: h 23 ASP cc_start: 0.7954 (m-30) cc_final: 0.7115 (m-30) REVERT: h 44 LEU cc_start: 0.9065 (mt) cc_final: 0.8845 (mt) REVERT: h 83 LEU cc_start: 0.8901 (mt) cc_final: 0.8524 (mt) REVERT: l 5 LYS cc_start: 0.8800 (mttm) cc_final: 0.8216 (mtmt) REVERT: l 40 LYS cc_start: 0.9420 (mtmt) cc_final: 0.9211 (mttt) REVERT: l 48 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8457 (mmmt) REVERT: m 78 ILE cc_start: 0.6335 (tp) cc_final: 0.6056 (tp) REVERT: n 14 LYS cc_start: 0.8358 (mtpt) cc_final: 0.7973 (mmtt) REVERT: p 17 ARG cc_start: 0.8348 (mpp80) cc_final: 0.8009 (mtp180) REVERT: p 47 MET cc_start: 0.6186 (tpt) cc_final: 0.5102 (tpt) REVERT: p 49 ARG cc_start: 0.7188 (ttt-90) cc_final: 0.5524 (ppt170) REVERT: p 52 VAL cc_start: 0.7707 (p) cc_final: 0.7183 (p) REVERT: p 79 VAL cc_start: 0.7775 (t) cc_final: 0.7472 (p) REVERT: p 86 LEU cc_start: 0.7045 (mt) cc_final: 0.6813 (mt) REVERT: r 8 MET cc_start: 0.7126 (ttm) cc_final: 0.6118 (ttm) REVERT: r 90 LEU cc_start: 0.6862 (mp) cc_final: 0.6600 (mt) REVERT: r 113 ARG cc_start: 0.6143 (mmt180) cc_final: 0.5434 (mmm160) REVERT: s 177 MET cc_start: 0.3681 (mmm) cc_final: 0.3373 (mtt) REVERT: s 185 PHE cc_start: 0.8169 (m-80) cc_final: 0.7934 (m-80) REVERT: x 65 MET cc_start: 0.8418 (ptm) cc_final: 0.8146 (ptm) REVERT: x 98 LYS cc_start: 0.7307 (mptt) cc_final: 0.7102 (mmtm) REVERT: x 113 ASN cc_start: 0.5673 (m-40) cc_final: 0.5317 (t0) REVERT: x 121 MET cc_start: 0.8472 (tpt) cc_final: 0.8181 (tpp) REVERT: x 161 ILE cc_start: 0.7408 (mm) cc_final: 0.7015 (mt) REVERT: x 165 LEU cc_start: 0.9358 (mt) cc_final: 0.9027 (mt) REVERT: x 179 ILE cc_start: 0.8314 (mt) cc_final: 0.7923 (mt) REVERT: x 182 PHE cc_start: 0.7504 (m-10) cc_final: 0.7276 (m-10) REVERT: x 185 THR cc_start: 0.8967 (p) cc_final: 0.8622 (p) REVERT: x 194 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8917 (mmmm) REVERT: x 267 ILE cc_start: 0.7788 (mm) cc_final: 0.7576 (mm) REVERT: x 294 GLN cc_start: 0.8787 (mt0) cc_final: 0.8519 (mt0) REVERT: x 389 ASP cc_start: 0.8167 (m-30) cc_final: 0.7896 (m-30) REVERT: x 399 MET cc_start: 0.8270 (tpt) cc_final: 0.7534 (tpt) REVERT: x 401 MET cc_start: 0.8590 (ppp) cc_final: 0.7851 (ppp) REVERT: x 453 ILE cc_start: 0.9401 (mt) cc_final: 0.9188 (mt) REVERT: y 23 LYS cc_start: 0.8227 (mmpt) cc_final: 0.8016 (mmmt) REVERT: y 38 MET cc_start: 0.8985 (tpp) cc_final: 0.8738 (mtt) REVERT: z 76 MET cc_start: 0.6203 (pmm) cc_final: 0.5431 (mmt) REVERT: 3 42 PHE cc_start: 0.9541 (p90) cc_final: 0.9304 (p90) REVERT: 3 53 ILE cc_start: 0.9164 (mt) cc_final: 0.8949 (mm) REVERT: 3 104 LEU cc_start: 0.8812 (mt) cc_final: 0.8321 (mt) REVERT: 3 118 PHE cc_start: 0.6383 (m-80) cc_final: 0.5040 (m-80) REVERT: 3 119 LEU cc_start: 0.7700 (mt) cc_final: 0.7254 (mt) REVERT: 3 139 MET cc_start: 0.7531 (mtp) cc_final: 0.6670 (mtp) REVERT: 3 140 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7699 (mmm160) REVERT: 3 143 LEU cc_start: 0.8819 (mp) cc_final: 0.8440 (mp) REVERT: 4 25 TYR cc_start: 0.8226 (t80) cc_final: 0.8014 (t80) REVERT: 5 55 ARG cc_start: 0.9442 (ttp80) cc_final: 0.8628 (ttm110) REVERT: 5 176 MET cc_start: 0.8965 (ttm) cc_final: 0.7129 (ttt) REVERT: 5 180 TYR cc_start: 0.8457 (m-80) cc_final: 0.7559 (m-80) REVERT: 5 349 VAL cc_start: 0.8710 (p) cc_final: 0.8172 (p) REVERT: 5 367 LEU cc_start: 0.9412 (mm) cc_final: 0.8819 (mm) REVERT: 5 370 MET cc_start: 0.7375 (mmp) cc_final: 0.7004 (mmp) REVERT: 5 376 TYR cc_start: 0.8636 (t80) cc_final: 0.8029 (t80) REVERT: 5 379 PHE cc_start: 0.9029 (m-10) cc_final: 0.8800 (m-10) REVERT: 5 407 MET cc_start: 0.9110 (tpp) cc_final: 0.8618 (tpp) REVERT: 5 414 MET cc_start: 0.8377 (mmp) cc_final: 0.7778 (mmp) REVERT: 5 415 CYS cc_start: 0.8648 (m) cc_final: 0.8111 (t) REVERT: 5 431 LYS cc_start: 0.8794 (tppt) cc_final: 0.8569 (tppt) REVERT: 5 467 PHE cc_start: 0.8630 (t80) cc_final: 0.7991 (t80) REVERT: 5 526 TRP cc_start: 0.8427 (p-90) cc_final: 0.7924 (p-90) REVERT: 5 532 ILE cc_start: 0.7712 (tp) cc_final: 0.7495 (tp) REVERT: 5 607 ASP cc_start: 0.8676 (p0) cc_final: 0.8419 (p0) outliers start: 3 outliers final: 0 residues processed: 1455 average time/residue: 1.2351 time to fit residues: 3045.6918 Evaluate side-chains 1179 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1178 time to evaluate : 6.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 1141 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 674 optimal weight: 20.0000 chunk 864 optimal weight: 40.0000 chunk 670 optimal weight: 10.0000 chunk 996 optimal weight: 20.0000 chunk 661 optimal weight: 20.0000 chunk 1179 optimal weight: 6.9990 chunk 738 optimal weight: 30.0000 chunk 719 optimal weight: 30.0000 chunk 544 optimal weight: 20.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS C 38 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN D 175 HIS D 198 HIS ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN O 5 GLN P 56 GLN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 HIS W 17 HIS ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 93 ASN Y 20 ASN ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 ASN ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 ASN ** g 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 110 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN l 43 HIS ** m 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 HIS ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 ASN ** r 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 149 HIS ** x 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 47 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 244 ASN ** x 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 63 ASN ** z 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 26 HIS ** 5 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 104 HIS ** 5 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 636 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 163182 Z= 0.468 Angle : 1.032 18.765 239544 Z= 0.513 Chirality : 0.052 0.320 29845 Planarity : 0.008 0.173 15619 Dihedral : 26.013 179.961 72307 Min Nonbonded Distance : 1.347 Molprobity Statistics. All-atom Clashscore : 44.62 Ramachandran Plot: Outliers : 0.60 % Allowed : 10.56 % Favored : 88.84 % Rotamer: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.92 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.48 % 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: -2.31 (0.09), residues: 8147 helix: -0.71 (0.08), residues: 3211 sheet: -1.64 (0.16), residues: 843 loop : -2.20 (0.09), residues: 4093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP x 379 HIS 0.025 0.003 HIS 5 267 PHE 0.057 0.004 PHE O 57 TYR 0.053 0.004 TYR P 130 ARG 0.031 0.001 ARG x 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1403 time to evaluate : 6.850 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: A 16 PHE cc_start: 0.8807 (m-80) cc_final: 0.8198 (m-80) REVERT: A 158 ILE cc_start: 0.8847 (mp) cc_final: 0.8469 (mp) REVERT: A 162 ASN cc_start: 0.5703 (OUTLIER) cc_final: 0.5227 (p0) REVERT: A 196 TRP cc_start: 0.8689 (t60) cc_final: 0.8047 (t60) REVERT: A 200 ARG cc_start: 0.8769 (mpp80) cc_final: 0.8544 (mpp80) REVERT: A 204 MET cc_start: 0.9366 (mtm) cc_final: 0.9050 (mtm) REVERT: A 237 LEU cc_start: 0.7671 (mt) cc_final: 0.7377 (mt) REVERT: A 241 ARG cc_start: 0.7451 (mtt-85) cc_final: 0.7238 (mtt-85) REVERT: B 168 MET cc_start: 0.6925 (ttm) cc_final: 0.6406 (ttm) REVERT: D 51 MET cc_start: 0.6236 (tmm) cc_final: 0.6029 (tmm) REVERT: D 115 MET cc_start: 0.7457 (mmp) cc_final: 0.6905 (mmm) REVERT: D 244 HIS cc_start: 0.6935 (m90) cc_final: 0.6708 (m90) REVERT: E 58 MET cc_start: 0.3003 (mtt) cc_final: 0.2103 (ttm) REVERT: E 112 TYR cc_start: 0.4783 (m-80) cc_final: 0.4552 (m-10) REVERT: F 43 MET cc_start: 0.4961 (mtm) cc_final: 0.4714 (mtm) REVERT: F 76 MET cc_start: 0.7449 (ttp) cc_final: 0.7157 (ttp) REVERT: F 149 LEU cc_start: 0.6829 (tp) cc_final: 0.6604 (tp) REVERT: F 192 LEU cc_start: 0.8845 (mt) cc_final: 0.8447 (tp) REVERT: F 234 ASP cc_start: 0.8391 (m-30) cc_final: 0.8098 (m-30) REVERT: H 120 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6070 (tp30) REVERT: H 143 GLU cc_start: 0.6991 (tp30) cc_final: 0.6420 (tp30) REVERT: J 20 LEU cc_start: 0.7986 (tp) cc_final: 0.7783 (tp) REVERT: J 163 MET cc_start: 0.7778 (ppp) cc_final: 0.7562 (ppp) REVERT: L 8 MET cc_start: 0.5135 (mtt) cc_final: 0.3293 (mtp) REVERT: L 25 TRP cc_start: 0.7165 (m100) cc_final: 0.6915 (m100) REVERT: L 33 ILE cc_start: 0.8242 (mm) cc_final: 0.7403 (mm) REVERT: L 37 LYS cc_start: 0.8567 (mmtt) cc_final: 0.7897 (mmtp) REVERT: M 118 MET cc_start: 0.7399 (mmp) cc_final: 0.6719 (mmp) REVERT: O 5 GLN cc_start: 0.5471 (OUTLIER) cc_final: 0.3177 (mt0) REVERT: O 16 LEU cc_start: 0.7441 (mt) cc_final: 0.7005 (mt) REVERT: O 118 MET cc_start: 0.7728 (mmp) cc_final: 0.6687 (mtm) REVERT: P 94 MET cc_start: 0.7524 (tpt) cc_final: 0.7242 (tpt) REVERT: P 149 ILE cc_start: 0.6248 (mm) cc_final: 0.5773 (mm) REVERT: Q 4 ASP cc_start: 0.8169 (p0) cc_final: 0.7820 (p0) REVERT: R 7 GLN cc_start: 0.9196 (mp10) cc_final: 0.8744 (mm-40) REVERT: R 20 LYS cc_start: 0.8042 (ptmt) cc_final: 0.7482 (mtmm) REVERT: R 45 ILE cc_start: 0.8679 (mm) cc_final: 0.8385 (tp) REVERT: R 66 ASN cc_start: 0.7845 (m-40) cc_final: 0.7589 (m110) REVERT: R 75 HIS cc_start: 0.7453 (m90) cc_final: 0.6927 (m90) REVERT: R 76 MET cc_start: 0.7716 (ptt) cc_final: 0.7486 (ptt) REVERT: R 89 MET cc_start: 0.7943 (tpt) cc_final: 0.7619 (ttt) REVERT: R 99 MET cc_start: 0.5604 (mmp) cc_final: 0.5118 (mmt) REVERT: S 93 MET cc_start: 0.7494 (tmm) cc_final: 0.6925 (tmm) REVERT: T 52 MET cc_start: 0.5650 (tpp) cc_final: 0.5304 (tpp) REVERT: T 65 TYR cc_start: 0.7797 (p90) cc_final: 0.7198 (p90) REVERT: U 42 PHE cc_start: 0.7897 (t80) cc_final: 0.7565 (t80) REVERT: U 75 GLU cc_start: 0.8299 (mp0) cc_final: 0.7762 (pm20) REVERT: U 85 TYR cc_start: 0.7441 (t80) cc_final: 0.6787 (t80) REVERT: U 90 TYR cc_start: 0.7962 (t80) cc_final: 0.7697 (t80) REVERT: U 94 ASN cc_start: 0.8706 (m-40) cc_final: 0.8437 (t0) REVERT: U 96 LEU cc_start: 0.7746 (mt) cc_final: 0.7457 (mt) REVERT: U 105 ASN cc_start: 0.6230 (m-40) cc_final: 0.6024 (m-40) REVERT: W 21 TYR cc_start: 0.6293 (t80) cc_final: 0.5943 (t80) REVERT: W 23 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7192 (mmm-85) REVERT: X 68 ARG cc_start: 0.8543 (tmm-80) cc_final: 0.8245 (tmm-80) REVERT: X 79 PHE cc_start: 0.7939 (p90) cc_final: 0.7241 (p90) REVERT: X 98 PHE cc_start: 0.8430 (m-80) cc_final: 0.8184 (m-80) REVERT: X 128 ILE cc_start: 0.8550 (mm) cc_final: 0.8265 (mm) REVERT: Y 3 PHE cc_start: 0.6275 (m-80) cc_final: 0.6042 (m-80) REVERT: Y 37 GLU cc_start: 0.7164 (pm20) cc_final: 0.6853 (pm20) REVERT: Z 5 MET cc_start: 0.6009 (mpp) cc_final: 0.5786 (mpp) REVERT: a 112 LEU cc_start: 0.9127 (mt) cc_final: 0.8705 (mp) REVERT: c 22 MET cc_start: 0.7416 (mmp) cc_final: 0.6578 (tpt) REVERT: d 22 THR cc_start: 0.8185 (p) cc_final: 0.7910 (p) REVERT: e 4 LEU cc_start: 0.7030 (mm) cc_final: 0.6718 (mm) REVERT: e 23 HIS cc_start: 0.6342 (t70) cc_final: 0.6139 (t70) REVERT: e 69 MET cc_start: 0.5941 (ttm) cc_final: 0.5392 (mmt) REVERT: g 10 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.8084 (ttm110) REVERT: g 34 TYR cc_start: 0.8390 (m-80) cc_final: 0.7798 (m-80) REVERT: g 82 MET cc_start: 0.6300 (ttt) cc_final: 0.5949 (mtp) REVERT: h 23 ASP cc_start: 0.8013 (m-30) cc_final: 0.7355 (m-30) REVERT: h 83 LEU cc_start: 0.9051 (mt) cc_final: 0.8585 (mt) REVERT: h 113 LEU cc_start: 0.7323 (mt) cc_final: 0.7105 (mt) REVERT: l 16 LYS cc_start: 0.9455 (mmtm) cc_final: 0.8685 (mmmt) REVERT: l 19 GLN cc_start: 0.8934 (mt0) cc_final: 0.8618 (mt0) REVERT: l 35 ILE cc_start: 0.8852 (mt) cc_final: 0.8476 (mm) REVERT: n 14 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8063 (mmtt) REVERT: o 45 GLN cc_start: 0.7989 (mm110) cc_final: 0.7766 (tm-30) REVERT: o 52 THR cc_start: 0.8085 (p) cc_final: 0.7792 (p) REVERT: p 17 ARG cc_start: 0.8122 (mpp80) cc_final: 0.7855 (mtp85) REVERT: p 79 VAL cc_start: 0.7957 (t) cc_final: 0.7687 (p) REVERT: p 86 LEU cc_start: 0.7176 (mt) cc_final: 0.6947 (mt) REVERT: r 8 MET cc_start: 0.7114 (ttm) cc_final: 0.6223 (ttm) REVERT: r 48 THR cc_start: 0.7878 (p) cc_final: 0.7487 (p) REVERT: s 45 MET cc_start: -0.1105 (mmm) cc_final: -0.1366 (mmp) REVERT: s 135 THR cc_start: 0.0588 (p) cc_final: 0.0165 (p) REVERT: s 177 MET cc_start: 0.3743 (mmm) cc_final: 0.3433 (mtt) REVERT: x 65 MET cc_start: 0.8738 (ptm) cc_final: 0.8414 (ptm) REVERT: x 113 ASN cc_start: 0.5350 (m-40) cc_final: 0.4766 (t0) REVERT: x 121 MET cc_start: 0.8503 (tpt) cc_final: 0.8217 (tpp) REVERT: x 165 LEU cc_start: 0.9391 (mt) cc_final: 0.9099 (mt) REVERT: x 179 ILE cc_start: 0.8469 (mt) cc_final: 0.8079 (mt) REVERT: x 183 ILE cc_start: 0.9123 (mm) cc_final: 0.8922 (mm) REVERT: x 269 SER cc_start: 0.9066 (p) cc_final: 0.8564 (p) REVERT: x 272 TYR cc_start: 0.7966 (m-80) cc_final: 0.7727 (m-80) REVERT: x 288 ASN cc_start: 0.7951 (m110) cc_final: 0.7659 (m110) REVERT: x 294 GLN cc_start: 0.9133 (mt0) cc_final: 0.8807 (mt0) REVERT: x 389 ASP cc_start: 0.8384 (m-30) cc_final: 0.8141 (m-30) REVERT: x 399 MET cc_start: 0.8547 (tpt) cc_final: 0.8108 (tpt) REVERT: x 401 MET cc_start: 0.9027 (ppp) cc_final: 0.8529 (ppp) REVERT: y 38 MET cc_start: 0.9035 (tpp) cc_final: 0.8794 (mtt) REVERT: z 76 MET cc_start: 0.5924 (pmm) cc_final: 0.5189 (mmt) REVERT: z 87 LEU cc_start: 0.8148 (mm) cc_final: 0.7938 (mp) REVERT: 3 96 MET cc_start: 0.8305 (ptp) cc_final: 0.8050 (ptp) REVERT: 3 104 LEU cc_start: 0.9000 (mt) cc_final: 0.8563 (mt) REVERT: 3 118 PHE cc_start: 0.6890 (m-80) cc_final: 0.5516 (m-80) REVERT: 3 119 LEU cc_start: 0.7678 (mt) cc_final: 0.7216 (mp) REVERT: 3 139 MET cc_start: 0.7734 (mtp) cc_final: 0.7079 (mtp) REVERT: 5 55 ARG cc_start: 0.9352 (ttp80) cc_final: 0.8559 (ttm110) REVERT: 5 127 THR cc_start: 0.8990 (p) cc_final: 0.8732 (p) REVERT: 5 133 HIS cc_start: 0.9013 (m90) cc_final: 0.8546 (m90) REVERT: 5 184 ILE cc_start: 0.9226 (pt) cc_final: 0.8860 (pt) REVERT: 5 205 MET cc_start: 0.9326 (tmm) cc_final: 0.8987 (tmm) REVERT: 5 212 TYR cc_start: 0.8012 (p90) cc_final: 0.7787 (p90) REVERT: 5 240 TYR cc_start: 0.8791 (t80) cc_final: 0.8383 (t80) REVERT: 5 370 MET cc_start: 0.7541 (mmp) cc_final: 0.7205 (mmp) REVERT: 5 371 PHE cc_start: 0.8153 (t80) cc_final: 0.7564 (t80) REVERT: 5 407 MET cc_start: 0.8966 (tpp) cc_final: 0.8347 (tpp) REVERT: 5 417 LEU cc_start: 0.9377 (mt) cc_final: 0.8692 (mt) REVERT: 5 430 MET cc_start: 0.8195 (ptm) cc_final: 0.7649 (ptm) REVERT: 5 431 LYS cc_start: 0.8832 (tppt) cc_final: 0.8523 (tppt) REVERT: 5 471 TYR cc_start: 0.8716 (t80) cc_final: 0.8508 (t80) REVERT: 5 473 PHE cc_start: 0.9292 (m-80) cc_final: 0.8777 (m-80) REVERT: 5 559 MET cc_start: 0.7791 (tpt) cc_final: 0.7220 (tpt) outliers start: 3 outliers final: 0 residues processed: 1405 average time/residue: 1.2688 time to fit residues: 3050.8661 Evaluate side-chains 1122 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1120 time to evaluate : 6.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 729 optimal weight: 20.0000 chunk 471 optimal weight: 20.0000 chunk 704 optimal weight: 20.0000 chunk 355 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 750 optimal weight: 20.0000 chunk 803 optimal weight: 9.9990 chunk 583 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 927 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN F 65 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 163 GLN I 100 ASN ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN P 25 HIS P 28 ASN ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 188 ASN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 HIS ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 HIS X 105 ASN Y 20 ASN ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 ASN ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 HIS ** n 22 GLN ** 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 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 47 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 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 411 HIS y 13 GLN y 63 ASN ** z 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 163182 Z= 0.325 Angle : 0.855 14.594 239544 Z= 0.430 Chirality : 0.044 0.315 29845 Planarity : 0.007 0.153 15619 Dihedral : 25.952 179.317 72307 Min Nonbonded Distance : 0.983 Molprobity Statistics. All-atom Clashscore : 35.09 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.49 % Favored : 89.93 % Rotamer: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.78 % 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: -2.12 (0.09), residues: 8147 helix: -0.53 (0.09), residues: 3193 sheet: -1.56 (0.16), residues: 849 loop : -2.11 (0.09), residues: 4105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP x 379 HIS 0.020 0.002 HIS 5 267 PHE 0.050 0.003 PHE S 175 TYR 0.035 0.003 TYR x 455 ARG 0.044 0.001 ARG y 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1415 time to evaluate : 6.778 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: A 16 PHE cc_start: 0.8716 (m-80) cc_final: 0.8114 (m-80) REVERT: A 162 ASN cc_start: 0.5685 (OUTLIER) cc_final: 0.5381 (p0) REVERT: A 196 TRP cc_start: 0.8680 (t60) cc_final: 0.8124 (t60) REVERT: A 198 ARG cc_start: 0.6999 (tpt-90) cc_final: 0.6785 (tpt170) REVERT: A 204 MET cc_start: 0.9324 (mtm) cc_final: 0.8996 (ttm) REVERT: A 228 ASP cc_start: 0.8587 (t70) cc_final: 0.8363 (t70) REVERT: A 241 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7320 (mtt-85) REVERT: B 168 MET cc_start: 0.6826 (ttm) cc_final: 0.6378 (ttm) REVERT: B 383 GLU cc_start: 0.8903 (pp20) cc_final: 0.8538 (pm20) REVERT: C 347 HIS cc_start: 0.6869 (t70) cc_final: 0.6638 (t70) REVERT: D 51 MET cc_start: 0.6258 (tmm) cc_final: 0.6044 (tmm) REVERT: D 115 MET cc_start: 0.7471 (mmp) cc_final: 0.6850 (mmm) REVERT: E 58 MET cc_start: 0.2910 (mtt) cc_final: 0.2023 (mtm) REVERT: E 112 TYR cc_start: 0.4371 (m-80) cc_final: 0.4119 (m-10) REVERT: E 165 SER cc_start: 0.6990 (p) cc_final: 0.6714 (t) REVERT: F 43 MET cc_start: 0.5010 (mtm) cc_final: 0.4787 (mtm) REVERT: F 76 MET cc_start: 0.7247 (ttp) cc_final: 0.6614 (ttp) REVERT: F 192 LEU cc_start: 0.8731 (mt) cc_final: 0.8326 (tp) REVERT: F 234 ASP cc_start: 0.8260 (m-30) cc_final: 0.7874 (m-30) REVERT: H 92 MET cc_start: 0.4406 (ttm) cc_final: 0.3073 (ttm) REVERT: H 113 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8086 (mp0) REVERT: H 143 GLU cc_start: 0.7041 (tp30) cc_final: 0.6419 (tp30) REVERT: J 163 MET cc_start: 0.7806 (ppp) cc_final: 0.7461 (ppp) REVERT: L 8 MET cc_start: 0.4989 (mtt) cc_final: 0.2994 (mtp) REVERT: L 37 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8313 (mmtp) REVERT: M 118 MET cc_start: 0.7314 (mmp) cc_final: 0.6578 (mmp) REVERT: N 91 GLN cc_start: 0.6899 (tt0) cc_final: 0.6632 (tt0) REVERT: O 5 GLN cc_start: 0.5450 (OUTLIER) cc_final: 0.3155 (mt0) REVERT: O 99 LEU cc_start: 0.4326 (tp) cc_final: 0.4083 (tt) REVERT: P 94 MET cc_start: 0.7476 (tpt) cc_final: 0.7059 (tpt) REVERT: P 144 CYS cc_start: 0.5538 (t) cc_final: 0.4957 (t) REVERT: Q 26 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7473 (mtt-85) REVERT: R 7 GLN cc_start: 0.9150 (mp10) cc_final: 0.8617 (mm-40) REVERT: R 15 LEU cc_start: 0.8456 (mt) cc_final: 0.8182 (mt) REVERT: R 19 LYS cc_start: 0.8700 (pptt) cc_final: 0.8455 (pptt) REVERT: R 45 ILE cc_start: 0.8562 (mm) cc_final: 0.8253 (tp) REVERT: R 66 ASN cc_start: 0.7821 (m-40) cc_final: 0.7560 (m110) REVERT: R 75 HIS cc_start: 0.7851 (m90) cc_final: 0.7343 (m90) REVERT: R 76 MET cc_start: 0.7658 (ptt) cc_final: 0.7439 (ptt) REVERT: R 80 LYS cc_start: 0.7948 (mmpt) cc_final: 0.7630 (mmmt) REVERT: R 89 MET cc_start: 0.7714 (tpt) cc_final: 0.7320 (ttm) REVERT: R 99 MET cc_start: 0.5525 (mmp) cc_final: 0.5171 (mmt) REVERT: S 93 MET cc_start: 0.7613 (tmm) cc_final: 0.6805 (tmm) REVERT: S 167 PHE cc_start: 0.6140 (m-80) cc_final: 0.5896 (m-80) REVERT: T 14 MET cc_start: 0.7929 (tpp) cc_final: 0.7673 (tpp) REVERT: T 52 MET cc_start: 0.5577 (tpp) cc_final: 0.5315 (tpp) REVERT: T 65 TYR cc_start: 0.7952 (p90) cc_final: 0.7360 (p90) REVERT: U 42 PHE cc_start: 0.7772 (t80) cc_final: 0.7350 (t80) REVERT: U 75 GLU cc_start: 0.7871 (mp0) cc_final: 0.7411 (pm20) REVERT: U 85 TYR cc_start: 0.6820 (t80) cc_final: 0.6609 (t80) REVERT: U 90 TYR cc_start: 0.7893 (t80) cc_final: 0.7477 (t80) REVERT: V 14 PHE cc_start: 0.7745 (m-10) cc_final: 0.7430 (m-10) REVERT: V 39 ILE cc_start: 0.9381 (mp) cc_final: 0.9151 (mp) REVERT: V 74 LYS cc_start: 0.9380 (mppt) cc_final: 0.9092 (mmmt) REVERT: V 85 ARG cc_start: 0.8883 (ttm110) cc_final: 0.8144 (mtt90) REVERT: V 124 GLU cc_start: 0.8146 (mp0) cc_final: 0.7945 (mp0) REVERT: W 23 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.7288 (mmm-85) REVERT: X 68 ARG cc_start: 0.8565 (tmm-80) cc_final: 0.8237 (tmm-80) REVERT: X 79 PHE cc_start: 0.7688 (p90) cc_final: 0.7308 (p90) REVERT: Z 5 MET cc_start: 0.6353 (mpp) cc_final: 0.5889 (mpp) REVERT: a 6 ARG cc_start: 0.8779 (mmt180) cc_final: 0.8205 (mmm160) REVERT: a 78 LEU cc_start: 0.6843 (mt) cc_final: 0.6531 (mt) REVERT: a 81 LEU cc_start: 0.6843 (mp) cc_final: 0.6444 (tp) REVERT: a 112 LEU cc_start: 0.9073 (mt) cc_final: 0.8671 (mp) REVERT: b 61 ASN cc_start: 0.7398 (m110) cc_final: 0.7019 (p0) REVERT: c 22 MET cc_start: 0.7133 (mmp) cc_final: 0.6507 (tpt) REVERT: d 61 ASP cc_start: 0.8201 (t0) cc_final: 0.7205 (p0) REVERT: e 4 LEU cc_start: 0.7240 (mm) cc_final: 0.6727 (mm) REVERT: e 69 MET cc_start: 0.5938 (ttm) cc_final: 0.5534 (mmt) REVERT: e 85 LEU cc_start: 0.6670 (pt) cc_final: 0.6409 (pt) REVERT: g 10 ARG cc_start: 0.8226 (mtt-85) cc_final: 0.7944 (ttm110) REVERT: g 34 TYR cc_start: 0.8366 (m-80) cc_final: 0.7757 (m-80) REVERT: g 82 MET cc_start: 0.6357 (ttt) cc_final: 0.5958 (mtp) REVERT: h 23 ASP cc_start: 0.7973 (m-30) cc_final: 0.7347 (m-30) REVERT: h 26 VAL cc_start: 0.8365 (t) cc_final: 0.7992 (t) REVERT: h 48 ARG cc_start: 0.9561 (ptt-90) cc_final: 0.9142 (ptt180) REVERT: h 83 LEU cc_start: 0.8921 (mt) cc_final: 0.8431 (mt) REVERT: k 10 ASP cc_start: 0.5689 (m-30) cc_final: 0.5292 (m-30) REVERT: l 30 LYS cc_start: 0.7430 (tmtt) cc_final: 0.7096 (tptt) REVERT: l 48 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8407 (mmmt) REVERT: n 14 LYS cc_start: 0.8301 (mtpt) cc_final: 0.7887 (mmtt) REVERT: n 20 MET cc_start: 0.9006 (tmm) cc_final: 0.8684 (tmm) REVERT: o 52 THR cc_start: 0.7898 (p) cc_final: 0.7626 (p) REVERT: p 47 MET cc_start: 0.6931 (tpt) cc_final: 0.6310 (tpt) REVERT: p 86 LEU cc_start: 0.7171 (mt) cc_final: 0.6910 (mt) REVERT: r 8 MET cc_start: 0.7045 (ttm) cc_final: 0.6171 (ttm) REVERT: r 113 ARG cc_start: 0.6293 (mmt180) cc_final: 0.5856 (mmm160) REVERT: s 177 MET cc_start: 0.3966 (mmm) cc_final: 0.3655 (mtt) REVERT: x 65 MET cc_start: 0.8759 (ptm) cc_final: 0.8448 (ptm) REVERT: x 113 ASN cc_start: 0.4925 (m-40) cc_final: 0.4446 (t0) REVERT: x 121 MET cc_start: 0.8568 (tpt) cc_final: 0.7899 (tpp) REVERT: x 165 LEU cc_start: 0.9404 (mt) cc_final: 0.9137 (mt) REVERT: x 179 ILE cc_start: 0.8398 (mt) cc_final: 0.7911 (mt) REVERT: x 252 PHE cc_start: 0.9030 (m-10) cc_final: 0.8794 (m-10) REVERT: x 269 SER cc_start: 0.8917 (p) cc_final: 0.8603 (p) REVERT: x 389 ASP cc_start: 0.8297 (m-30) cc_final: 0.7945 (m-30) REVERT: x 399 MET cc_start: 0.8307 (tpt) cc_final: 0.8080 (tpt) REVERT: x 401 MET cc_start: 0.8900 (ppp) cc_final: 0.8616 (ppp) REVERT: y 23 LYS cc_start: 0.8266 (mmpt) cc_final: 0.8028 (mmmt) REVERT: y 38 MET cc_start: 0.8978 (tpp) cc_final: 0.8731 (mtt) REVERT: z 76 MET cc_start: 0.6097 (pmm) cc_final: 0.5386 (mmt) REVERT: z 87 LEU cc_start: 0.8124 (mm) cc_final: 0.7892 (mp) REVERT: 3 118 PHE cc_start: 0.6701 (m-80) cc_final: 0.5517 (m-80) REVERT: 3 119 LEU cc_start: 0.7719 (mt) cc_final: 0.7285 (mp) REVERT: 3 139 MET cc_start: 0.7524 (mtp) cc_final: 0.6897 (mtp) REVERT: 5 55 ARG cc_start: 0.9295 (ttp80) cc_final: 0.8494 (ttm110) REVERT: 5 133 HIS cc_start: 0.8999 (m90) cc_final: 0.8121 (m90) REVERT: 5 194 TRP cc_start: 0.7502 (t-100) cc_final: 0.7189 (t-100) REVERT: 5 205 MET cc_start: 0.9307 (tmm) cc_final: 0.9075 (tmm) REVERT: 5 240 TYR cc_start: 0.8639 (t80) cc_final: 0.8288 (t80) REVERT: 5 366 LEU cc_start: 0.9427 (tt) cc_final: 0.8814 (tt) REVERT: 5 370 MET cc_start: 0.7528 (mmp) cc_final: 0.7193 (mmp) REVERT: 5 371 PHE cc_start: 0.8131 (t80) cc_final: 0.7662 (t80) REVERT: 5 430 MET cc_start: 0.8333 (ptm) cc_final: 0.7727 (ptm) REVERT: 5 431 LYS cc_start: 0.8879 (tppt) cc_final: 0.8557 (tppt) REVERT: 5 469 ILE cc_start: 0.9507 (pt) cc_final: 0.9095 (pt) outliers start: 3 outliers final: 0 residues processed: 1417 average time/residue: 1.2404 time to fit residues: 2981.0063 Evaluate side-chains 1137 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1135 time to evaluate : 6.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 1073 optimal weight: 9.9990 chunk 1130 optimal weight: 30.0000 chunk 1031 optimal weight: 30.0000 chunk 1099 optimal weight: 1.9990 chunk 1129 optimal weight: 0.5980 chunk 661 optimal weight: 20.0000 chunk 478 optimal weight: 8.9990 chunk 863 optimal weight: 30.0000 chunk 337 optimal weight: 3.9990 chunk 993 optimal weight: 10.0000 chunk 1039 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN A 215 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 119 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 64 GLN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 188 ASN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 GLN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN V 77 HIS X 105 ASN Y 20 ASN ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 ASN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 HIS ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 102 GLN ** 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 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 147 HIS ** x 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 ASN ** 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 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 63 ASN ** z 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.7909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 163182 Z= 0.287 Angle : 0.821 15.275 239544 Z= 0.412 Chirality : 0.043 0.328 29845 Planarity : 0.007 0.134 15619 Dihedral : 25.897 179.935 72307 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 33.84 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.82 % Favored : 89.63 % Rotamer: Outliers : 0.04 % Allowed : 0.98 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.78 % 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: -2.00 (0.09), residues: 8147 helix: -0.39 (0.09), residues: 3186 sheet: -1.52 (0.16), residues: 824 loop : -2.06 (0.09), residues: 4137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP x 379 HIS 0.025 0.002 HIS 5 267 PHE 0.041 0.003 PHE D 180 TYR 0.052 0.003 TYR Z 122 ARG 0.020 0.001 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1390 time to evaluate : 6.379 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: A 3 ARG cc_start: 0.9240 (tpp80) cc_final: 0.8698 (ttp80) REVERT: A 16 PHE cc_start: 0.8626 (m-80) cc_final: 0.8037 (m-80) REVERT: A 162 ASN cc_start: 0.5509 (OUTLIER) cc_final: 0.5140 (p0) REVERT: A 196 TRP cc_start: 0.8640 (t60) cc_final: 0.8016 (t60) REVERT: A 198 ARG cc_start: 0.6948 (tpt-90) cc_final: 0.6706 (tpt170) REVERT: A 204 MET cc_start: 0.9321 (mtm) cc_final: 0.8954 (ttm) REVERT: A 228 ASP cc_start: 0.8611 (t70) cc_final: 0.8395 (t70) REVERT: A 241 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.7203 (mtt-85) REVERT: B 168 MET cc_start: 0.6250 (ttm) cc_final: 0.5402 (ttm) REVERT: B 322 HIS cc_start: 0.7124 (m170) cc_final: 0.6497 (m170) REVERT: B 383 GLU cc_start: 0.8881 (pp20) cc_final: 0.8514 (pm20) REVERT: C 46 LYS cc_start: 0.6788 (mttt) cc_final: 0.5725 (mptt) REVERT: D 51 MET cc_start: 0.6418 (tmm) cc_final: 0.6124 (tmm) REVERT: D 115 MET cc_start: 0.7371 (mmp) cc_final: 0.6799 (mmm) REVERT: E 165 SER cc_start: 0.7021 (p) cc_final: 0.6729 (t) REVERT: F 72 ARG cc_start: 0.7285 (tpm170) cc_final: 0.6482 (ttm170) REVERT: F 76 MET cc_start: 0.7237 (ttp) cc_final: 0.6676 (ttt) REVERT: F 84 TYR cc_start: 0.5648 (t80) cc_final: 0.5420 (t80) REVERT: F 192 LEU cc_start: 0.8893 (mt) cc_final: 0.8510 (tp) REVERT: F 234 ASP cc_start: 0.8290 (m-30) cc_final: 0.7885 (m-30) REVERT: H 55 LEU cc_start: 0.3911 (tp) cc_final: 0.3322 (pp) REVERT: H 92 MET cc_start: 0.3694 (ttm) cc_final: 0.3218 (ttm) REVERT: I 52 MET cc_start: 0.5846 (mmm) cc_final: 0.5583 (mmm) REVERT: J 163 MET cc_start: 0.7851 (ppp) cc_final: 0.7601 (ppp) REVERT: L 8 MET cc_start: 0.4640 (mtt) cc_final: 0.2772 (mtp) REVERT: L 37 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8234 (mmtp) REVERT: L 89 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7591 (mtmt) REVERT: M 118 MET cc_start: 0.7257 (mmp) cc_final: 0.6516 (mmp) REVERT: N 91 GLN cc_start: 0.6879 (tt0) cc_final: 0.6557 (tt0) REVERT: N 149 GLN cc_start: 0.5411 (pt0) cc_final: 0.4362 (pp30) REVERT: O 5 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.3329 (mt0) REVERT: O 99 LEU cc_start: 0.4499 (tp) cc_final: 0.4224 (tt) REVERT: P 18 ARG cc_start: 0.5907 (ttp80) cc_final: 0.5609 (ttp80) REVERT: P 50 ASP cc_start: 0.7605 (m-30) cc_final: 0.7311 (m-30) REVERT: P 86 LYS cc_start: 0.8470 (tppt) cc_final: 0.8074 (tppt) REVERT: P 121 LYS cc_start: 0.8825 (mppt) cc_final: 0.8586 (mptt) REVERT: P 144 CYS cc_start: 0.5295 (t) cc_final: 0.4606 (t) REVERT: P 151 THR cc_start: 0.6689 (t) cc_final: 0.6466 (m) REVERT: R 7 GLN cc_start: 0.9144 (mp10) cc_final: 0.8633 (mm-40) REVERT: R 28 GLU cc_start: 0.7237 (pt0) cc_final: 0.7033 (pt0) REVERT: R 45 ILE cc_start: 0.8506 (mm) cc_final: 0.8156 (tp) REVERT: R 66 ASN cc_start: 0.7656 (m-40) cc_final: 0.7410 (m110) REVERT: R 75 HIS cc_start: 0.8001 (m90) cc_final: 0.7224 (m170) REVERT: R 89 MET cc_start: 0.7511 (tpt) cc_final: 0.7178 (ttm) REVERT: R 95 TRP cc_start: 0.6078 (t-100) cc_final: 0.5762 (t60) REVERT: S 93 MET cc_start: 0.7874 (tmm) cc_final: 0.7075 (tmm) REVERT: T 52 MET cc_start: 0.5543 (tpp) cc_final: 0.5077 (tpp) REVERT: T 65 TYR cc_start: 0.7931 (p90) cc_final: 0.7352 (p90) REVERT: T 88 ARG cc_start: 0.7457 (ptp90) cc_final: 0.6933 (ptp90) REVERT: U 42 PHE cc_start: 0.7768 (t80) cc_final: 0.7386 (t80) REVERT: U 75 GLU cc_start: 0.8253 (mp0) cc_final: 0.7618 (pm20) REVERT: U 85 TYR cc_start: 0.6838 (t80) cc_final: 0.6139 (t80) REVERT: U 90 TYR cc_start: 0.8033 (t80) cc_final: 0.7420 (t80) REVERT: V 14 PHE cc_start: 0.7523 (m-10) cc_final: 0.7266 (m-10) REVERT: V 27 ASN cc_start: 0.8565 (p0) cc_final: 0.7681 (t0) REVERT: V 86 LYS cc_start: 0.8723 (tptt) cc_final: 0.7573 (tptt) REVERT: V 112 MET cc_start: 0.8548 (pmm) cc_final: 0.8032 (pmm) REVERT: W 23 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.7257 (mmm-85) REVERT: X 68 ARG cc_start: 0.8527 (tmm-80) cc_final: 0.8216 (tmm-80) REVERT: X 79 PHE cc_start: 0.7683 (p90) cc_final: 0.7352 (p90) REVERT: X 103 LYS cc_start: 0.8549 (mttt) cc_final: 0.8280 (mttt) REVERT: Z 5 MET cc_start: 0.6562 (mpp) cc_final: 0.6021 (mpp) REVERT: a 6 ARG cc_start: 0.8908 (mmt180) cc_final: 0.8414 (mmm160) REVERT: a 78 LEU cc_start: 0.6462 (mt) cc_final: 0.6032 (mt) REVERT: a 81 LEU cc_start: 0.6800 (mp) cc_final: 0.6400 (tp) REVERT: a 112 LEU cc_start: 0.9082 (mt) cc_final: 0.8686 (mp) REVERT: b 61 ASN cc_start: 0.7427 (m110) cc_final: 0.7059 (p0) REVERT: c 22 MET cc_start: 0.7150 (mmp) cc_final: 0.6288 (tpt) REVERT: c 77 ASN cc_start: 0.8773 (m-40) cc_final: 0.8518 (m-40) REVERT: d 61 ASP cc_start: 0.8234 (t0) cc_final: 0.7275 (p0) REVERT: d 93 ASN cc_start: 0.6072 (t0) cc_final: 0.4770 (t0) REVERT: d 96 GLU cc_start: 0.7930 (tp30) cc_final: 0.7621 (pt0) REVERT: e 60 TYR cc_start: 0.6813 (m-80) cc_final: 0.6540 (m-80) REVERT: e 69 MET cc_start: 0.5960 (ttm) cc_final: 0.5688 (mmm) REVERT: g 82 MET cc_start: 0.6340 (ttt) cc_final: 0.5928 (mtp) REVERT: h 23 ASP cc_start: 0.7925 (m-30) cc_final: 0.7533 (m-30) REVERT: h 30 GLN cc_start: 0.7236 (mp10) cc_final: 0.6926 (mp10) REVERT: h 44 LEU cc_start: 0.9223 (mt) cc_final: 0.8976 (mt) REVERT: h 83 LEU cc_start: 0.8884 (mt) cc_final: 0.8375 (mt) REVERT: k 25 ILE cc_start: 0.8431 (mm) cc_final: 0.8165 (mm) REVERT: l 48 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8449 (mmmt) REVERT: n 14 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7685 (mmtt) REVERT: n 20 MET cc_start: 0.9044 (tmm) cc_final: 0.8770 (tmm) REVERT: o 58 LYS cc_start: 0.7474 (mmtp) cc_final: 0.6710 (tptt) REVERT: p 47 MET cc_start: 0.6690 (tpt) cc_final: 0.6046 (tpt) REVERT: p 86 LEU cc_start: 0.7132 (mt) cc_final: 0.6922 (mt) REVERT: r 8 MET cc_start: 0.7030 (ttm) cc_final: 0.6115 (ttm) REVERT: r 97 ILE cc_start: 0.8249 (tp) cc_final: 0.8026 (tp) REVERT: r 113 ARG cc_start: 0.6292 (mmt180) cc_final: 0.5905 (mmm160) REVERT: s 60 MET cc_start: 0.2668 (mmm) cc_final: 0.2400 (mmm) REVERT: s 177 MET cc_start: 0.3776 (mmm) cc_final: 0.3473 (mtt) REVERT: x 65 MET cc_start: 0.8703 (ptm) cc_final: 0.8358 (ptm) REVERT: x 113 ASN cc_start: 0.4748 (m-40) cc_final: 0.4445 (t0) REVERT: x 121 MET cc_start: 0.8644 (tpt) cc_final: 0.7981 (tpp) REVERT: x 179 ILE cc_start: 0.8419 (mt) cc_final: 0.7806 (mt) REVERT: x 193 TRP cc_start: 0.8877 (m100) cc_final: 0.8648 (m-10) REVERT: x 213 ILE cc_start: 0.9471 (pt) cc_final: 0.9200 (mp) REVERT: x 269 SER cc_start: 0.8845 (p) cc_final: 0.8357 (p) REVERT: x 389 ASP cc_start: 0.8385 (m-30) cc_final: 0.7929 (m-30) REVERT: x 399 MET cc_start: 0.8236 (tpt) cc_final: 0.7967 (tpt) REVERT: x 401 MET cc_start: 0.8935 (ppp) cc_final: 0.8580 (ppp) REVERT: y 23 LYS cc_start: 0.8319 (mmpt) cc_final: 0.8086 (mmmt) REVERT: y 38 MET cc_start: 0.8989 (tpp) cc_final: 0.8743 (mtt) REVERT: z 76 MET cc_start: 0.6122 (pmm) cc_final: 0.5399 (mmt) REVERT: z 87 LEU cc_start: 0.8052 (mm) cc_final: 0.7837 (mt) REVERT: 3 104 LEU cc_start: 0.8943 (mt) cc_final: 0.8519 (mt) REVERT: 3 118 PHE cc_start: 0.6588 (m-80) cc_final: 0.5938 (m-80) REVERT: 3 122 PHE cc_start: 0.7044 (m-80) cc_final: 0.6798 (m-80) REVERT: 3 139 MET cc_start: 0.7510 (mtp) cc_final: 0.6904 (mtp) REVERT: 5 55 ARG cc_start: 0.9226 (ttp80) cc_final: 0.8433 (ttm110) REVERT: 5 127 THR cc_start: 0.8892 (p) cc_final: 0.8572 (p) REVERT: 5 133 HIS cc_start: 0.8990 (m90) cc_final: 0.8356 (m90) REVERT: 5 176 MET cc_start: 0.9010 (ttt) cc_final: 0.8787 (ttt) REVERT: 5 182 MET cc_start: 0.8579 (ttm) cc_final: 0.8262 (ttm) REVERT: 5 194 TRP cc_start: 0.7426 (t-100) cc_final: 0.7137 (t-100) REVERT: 5 240 TYR cc_start: 0.8546 (t80) cc_final: 0.8291 (t80) REVERT: 5 366 LEU cc_start: 0.9445 (tt) cc_final: 0.8419 (tt) REVERT: 5 367 LEU cc_start: 0.9062 (mm) cc_final: 0.8329 (mm) REVERT: 5 371 PHE cc_start: 0.8195 (t80) cc_final: 0.7266 (t80) REVERT: 5 375 LEU cc_start: 0.9614 (mt) cc_final: 0.9318 (mt) REVERT: 5 376 TYR cc_start: 0.8308 (t80) cc_final: 0.7693 (t80) REVERT: 5 414 MET cc_start: 0.8510 (mmp) cc_final: 0.8233 (mmp) REVERT: 5 430 MET cc_start: 0.8349 (ptm) cc_final: 0.7878 (ptm) REVERT: 5 431 LYS cc_start: 0.8883 (tppt) cc_final: 0.8579 (tppt) REVERT: 5 469 ILE cc_start: 0.9463 (pt) cc_final: 0.9002 (pt) REVERT: 5 501 ILE cc_start: 0.9293 (pt) cc_final: 0.9024 (mp) REVERT: 5 674 GLU cc_start: 0.8602 (tt0) cc_final: 0.8018 (mp0) outliers start: 3 outliers final: 0 residues processed: 1392 average time/residue: 1.2630 time to fit residues: 3015.4030 Evaluate side-chains 1124 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1122 time to evaluate : 6.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 1095 optimal weight: 0.9990 chunk 721 optimal weight: 30.0000 chunk 1162 optimal weight: 0.7980 chunk 709 optimal weight: 30.0000 chunk 551 optimal weight: 9.9990 chunk 808 optimal weight: 20.0000 chunk 1219 optimal weight: 10.0000 chunk 1122 optimal weight: 20.0000 chunk 971 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 750 optimal weight: 20.0000 overall best weight: 6.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN A 217 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 64 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN P 56 GLN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 188 ASN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Y 56 GLN Y 96 HIS ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 ASN ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN ** m 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 HIS ** n 22 GLN ** 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 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 95 HIS ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 72 ASN ** 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 218 HIS ** x 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 63 ASN ** z 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.8402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 163182 Z= 0.335 Angle : 0.874 15.335 239544 Z= 0.438 Chirality : 0.045 0.396 29845 Planarity : 0.007 0.155 15619 Dihedral : 25.984 179.936 72307 Min Nonbonded Distance : 0.970 Molprobity Statistics. All-atom Clashscore : 38.47 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.46 % Favored : 89.04 % Rotamer: Outliers : 0.07 % Allowed : 0.72 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.78 % 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: -2.20 (0.09), residues: 8147 helix: -0.59 (0.09), residues: 3169 sheet: -1.58 (0.16), residues: 850 loop : -2.16 (0.09), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.004 TRP S 81 HIS 0.025 0.002 HIS 5 267 PHE 0.042 0.003 PHE 4 10 TYR 0.054 0.003 TYR Z 122 ARG 0.018 0.001 ARG C 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16294 Ramachandran restraints generated. 8147 Oldfield, 0 Emsley, 8147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1353 time to evaluate : 6.674 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: A 16 PHE cc_start: 0.8654 (m-80) cc_final: 0.8030 (m-80) REVERT: A 162 ASN cc_start: 0.5331 (OUTLIER) cc_final: 0.5028 (p0) REVERT: A 196 TRP cc_start: 0.8718 (t60) cc_final: 0.7909 (t60) REVERT: A 198 ARG cc_start: 0.6873 (tpt-90) cc_final: 0.6669 (tpt170) REVERT: A 204 MET cc_start: 0.9290 (mtm) cc_final: 0.8924 (ttm) REVERT: A 228 ASP cc_start: 0.8397 (t70) cc_final: 0.8117 (t70) REVERT: A 237 LEU cc_start: 0.7692 (mt) cc_final: 0.7423 (mt) REVERT: A 241 ARG cc_start: 0.7473 (mtt-85) cc_final: 0.7268 (mtt-85) REVERT: B 168 MET cc_start: 0.6293 (ttm) cc_final: 0.5611 (ttm) REVERT: B 276 HIS cc_start: 0.6292 (t-90) cc_final: 0.6085 (t-90) REVERT: B 322 HIS cc_start: 0.7135 (m170) cc_final: 0.6542 (m170) REVERT: C 46 LYS cc_start: 0.6875 (mttt) cc_final: 0.5924 (mptt) REVERT: C 101 MET cc_start: 0.6849 (ttt) cc_final: 0.5779 (tpp) REVERT: D 51 MET cc_start: 0.6392 (tmm) cc_final: 0.6168 (tmm) REVERT: D 115 MET cc_start: 0.7401 (mmp) cc_final: 0.6826 (mmm) REVERT: D 208 MET cc_start: 0.5031 (mmp) cc_final: 0.4082 (mmm) REVERT: D 244 HIS cc_start: 0.6670 (m90) cc_final: 0.6413 (m90) REVERT: E 165 SER cc_start: 0.7095 (p) cc_final: 0.6797 (t) REVERT: F 192 LEU cc_start: 0.8862 (mt) cc_final: 0.8458 (tp) REVERT: F 234 ASP cc_start: 0.8173 (m-30) cc_final: 0.7795 (m-30) REVERT: G 187 LYS cc_start: 0.7128 (pttm) cc_final: 0.6824 (pttm) REVERT: H 55 LEU cc_start: 0.4141 (tp) cc_final: 0.3425 (pp) REVERT: H 92 MET cc_start: 0.4142 (ttm) cc_final: 0.3691 (ttm) REVERT: I 52 MET cc_start: 0.5654 (mmm) cc_final: 0.5368 (mmm) REVERT: J 20 LEU cc_start: 0.7924 (tp) cc_final: 0.7716 (tp) REVERT: J 163 MET cc_start: 0.7887 (ppp) cc_final: 0.7573 (ppp) REVERT: L 8 MET cc_start: 0.4290 (mtt) cc_final: 0.3067 (mtp) REVERT: L 37 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8230 (mmtp) REVERT: M 55 MET cc_start: 0.5800 (tpt) cc_final: 0.5562 (tpt) REVERT: M 118 MET cc_start: 0.7030 (mmp) cc_final: 0.6208 (mmp) REVERT: N 105 ARG cc_start: 0.7557 (ttm170) cc_final: 0.6977 (ttm170) REVERT: N 149 GLN cc_start: 0.5607 (pt0) cc_final: 0.4408 (pp30) REVERT: N 197 THR cc_start: 0.8684 (p) cc_final: 0.8456 (p) REVERT: O 5 GLN cc_start: 0.5309 (OUTLIER) cc_final: 0.3040 (mt0) REVERT: O 99 LEU cc_start: 0.4389 (tp) cc_final: 0.4071 (tt) REVERT: P 18 ARG cc_start: 0.5618 (ttp80) cc_final: 0.5345 (ttp80) REVERT: P 50 ASP cc_start: 0.7626 (m-30) cc_final: 0.7416 (m-30) REVERT: P 151 THR cc_start: 0.6620 (t) cc_final: 0.6390 (m) REVERT: Q 23 ILE cc_start: 0.6784 (mt) cc_final: 0.5782 (mt) REVERT: R 7 GLN cc_start: 0.9142 (mp10) cc_final: 0.8829 (mm-40) REVERT: R 15 LEU cc_start: 0.8509 (mt) cc_final: 0.8191 (mt) REVERT: R 45 ILE cc_start: 0.8430 (mm) cc_final: 0.8052 (tp) REVERT: R 66 ASN cc_start: 0.7728 (m-40) cc_final: 0.7448 (m110) REVERT: R 75 HIS cc_start: 0.8205 (m90) cc_final: 0.7399 (m170) REVERT: R 89 MET cc_start: 0.7416 (tpt) cc_final: 0.7154 (ttm) REVERT: T 14 MET cc_start: 0.7526 (tpp) cc_final: 0.7112 (tpp) REVERT: T 52 MET cc_start: 0.5807 (tpp) cc_final: 0.5171 (tpp) REVERT: T 65 TYR cc_start: 0.8016 (p90) cc_final: 0.7385 (p90) REVERT: U 75 GLU cc_start: 0.8448 (mp0) cc_final: 0.7838 (pm20) REVERT: U 85 TYR cc_start: 0.6776 (t80) cc_final: 0.6113 (t80) REVERT: U 90 TYR cc_start: 0.8213 (t80) cc_final: 0.7373 (t80) REVERT: V 86 LYS cc_start: 0.8689 (tptt) cc_final: 0.8396 (tptt) REVERT: V 112 MET cc_start: 0.8563 (pmm) cc_final: 0.7636 (pmm) REVERT: V 128 LEU cc_start: 0.5069 (tp) cc_final: 0.4490 (tp) REVERT: V 131 ARG cc_start: 0.8858 (tmt170) cc_final: 0.8623 (tpt-90) REVERT: W 20 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7653 (mmm-85) REVERT: W 23 ARG cc_start: 0.7436 (mmm-85) cc_final: 0.7168 (mmm-85) REVERT: X 68 ARG cc_start: 0.8559 (tmm-80) cc_final: 0.8271 (tmm-80) REVERT: X 79 PHE cc_start: 0.7683 (p90) cc_final: 0.7400 (p90) REVERT: X 98 PHE cc_start: 0.8020 (m-80) cc_final: 0.7726 (m-80) REVERT: Y 3 PHE cc_start: 0.6197 (m-80) cc_final: 0.5913 (m-80) REVERT: Y 38 LEU cc_start: 0.8367 (mm) cc_final: 0.8016 (mm) REVERT: Y 127 GLN cc_start: 0.6927 (pp30) cc_final: 0.6436 (mm110) REVERT: Z 5 MET cc_start: 0.6610 (mpp) cc_final: 0.6212 (mpp) REVERT: Z 116 VAL cc_start: 0.8840 (t) cc_final: 0.8390 (p) REVERT: a 6 ARG cc_start: 0.8905 (mmt180) cc_final: 0.8270 (tpp-160) REVERT: a 34 ASN cc_start: 0.7739 (m110) cc_final: 0.7509 (m110) REVERT: a 78 LEU cc_start: 0.6810 (mt) cc_final: 0.6199 (mt) REVERT: a 81 LEU cc_start: 0.6757 (mp) cc_final: 0.6277 (tp) REVERT: a 112 LEU cc_start: 0.9077 (mt) cc_final: 0.8695 (mp) REVERT: c 22 MET cc_start: 0.7008 (mmp) cc_final: 0.6383 (tpt) REVERT: d 61 ASP cc_start: 0.8287 (t0) cc_final: 0.7281 (p0) REVERT: e 4 LEU cc_start: 0.7485 (mm) cc_final: 0.6871 (mm) REVERT: e 60 TYR cc_start: 0.6970 (m-80) cc_final: 0.6612 (m-80) REVERT: e 89 LEU cc_start: 0.8049 (mt) cc_final: 0.7769 (mt) REVERT: e 90 MET cc_start: 0.7620 (pmm) cc_final: 0.6710 (pmm) REVERT: f 104 MET cc_start: 0.2220 (mtt) cc_final: 0.2016 (mtt) REVERT: g 82 MET cc_start: 0.6344 (ttt) cc_final: 0.5787 (mtp) REVERT: h 23 ASP cc_start: 0.7979 (m-30) cc_final: 0.7512 (m-30) REVERT: h 30 GLN cc_start: 0.6769 (mp10) cc_final: 0.6433 (mp10) REVERT: h 83 LEU cc_start: 0.8750 (mt) cc_final: 0.8360 (mt) REVERT: l 48 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8494 (mmmt) REVERT: n 14 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7554 (mmtt) REVERT: n 20 MET cc_start: 0.8992 (tmm) cc_final: 0.8738 (tmm) REVERT: o 52 THR cc_start: 0.7730 (p) cc_final: 0.7402 (p) REVERT: p 47 MET cc_start: 0.6529 (tpt) cc_final: 0.5842 (tpt) REVERT: p 49 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.5474 (ttt-90) REVERT: p 70 THR cc_start: 0.8421 (m) cc_final: 0.8128 (m) REVERT: r 8 MET cc_start: 0.7113 (ttm) cc_final: 0.6245 (ttm) REVERT: s 55 MET cc_start: -0.0186 (tpt) cc_final: -0.0451 (tpp) REVERT: s 177 MET cc_start: 0.3637 (mmm) cc_final: 0.3353 (mtt) REVERT: x 65 MET cc_start: 0.8713 (ptm) cc_final: 0.8301 (ptm) REVERT: x 113 ASN cc_start: 0.5074 (m-40) cc_final: 0.4527 (t0) REVERT: x 121 MET cc_start: 0.8633 (tpt) cc_final: 0.7925 (tpp) REVERT: x 179 ILE cc_start: 0.8452 (mt) cc_final: 0.7939 (mt) REVERT: x 189 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8506 (mt-10) REVERT: x 213 ILE cc_start: 0.9563 (pt) cc_final: 0.9308 (mp) REVERT: x 269 SER cc_start: 0.8862 (p) cc_final: 0.8392 (p) REVERT: x 307 MET cc_start: 0.8262 (ppp) cc_final: 0.7950 (ppp) REVERT: x 364 TYR cc_start: 0.8351 (t80) cc_final: 0.8050 (t80) REVERT: x 389 ASP cc_start: 0.8439 (m-30) cc_final: 0.8003 (m-30) REVERT: x 401 MET cc_start: 0.9179 (ppp) cc_final: 0.8536 (ppp) REVERT: y 23 LYS cc_start: 0.8271 (mmpt) cc_final: 0.8024 (mmmt) REVERT: y 38 MET cc_start: 0.8988 (tpp) cc_final: 0.8770 (mtt) REVERT: z 76 MET cc_start: 0.5818 (pmm) cc_final: 0.5124 (mmt) REVERT: z 87 LEU cc_start: 0.8089 (mm) cc_final: 0.7873 (mt) REVERT: 3 104 LEU cc_start: 0.9059 (mt) cc_final: 0.8700 (mt) REVERT: 3 118 PHE cc_start: 0.6431 (m-80) cc_final: 0.5984 (m-80) REVERT: 3 119 LEU cc_start: 0.7084 (mt) cc_final: 0.6715 (mp) REVERT: 3 139 MET cc_start: 0.7532 (mtp) cc_final: 0.6937 (mtp) REVERT: 5 55 ARG cc_start: 0.9240 (ttp80) cc_final: 0.8448 (ttm110) REVERT: 5 133 HIS cc_start: 0.8965 (m90) cc_final: 0.8350 (m90) REVERT: 5 176 MET cc_start: 0.8860 (ttt) cc_final: 0.8493 (ttm) REVERT: 5 182 MET cc_start: 0.8520 (ttm) cc_final: 0.8036 (ttm) REVERT: 5 194 TRP cc_start: 0.7340 (t-100) cc_final: 0.7063 (t-100) REVERT: 5 205 MET cc_start: 0.9234 (tmm) cc_final: 0.9001 (tmm) REVERT: 5 240 TYR cc_start: 0.8606 (t80) cc_final: 0.8191 (t80) REVERT: 5 367 LEU cc_start: 0.8765 (mm) cc_final: 0.8121 (mm) REVERT: 5 371 PHE cc_start: 0.8008 (t80) cc_final: 0.7708 (t80) REVERT: 5 407 MET cc_start: 0.8384 (mmm) cc_final: 0.8094 (mmm) REVERT: 5 414 MET cc_start: 0.8323 (mmp) cc_final: 0.8057 (mmp) REVERT: 5 430 MET cc_start: 0.8405 (ptm) cc_final: 0.7904 (ptm) REVERT: 5 431 LYS cc_start: 0.8876 (tppt) cc_final: 0.8528 (tppt) REVERT: 5 469 ILE cc_start: 0.9454 (pt) cc_final: 0.8987 (pt) REVERT: 5 473 PHE cc_start: 0.9289 (m-80) cc_final: 0.9065 (m-80) REVERT: 5 674 GLU cc_start: 0.8594 (tt0) cc_final: 0.8065 (mp0) outliers start: 5 outliers final: 2 residues processed: 1356 average time/residue: 1.3124 time to fit residues: 3065.2949 Evaluate side-chains 1123 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1119 time to evaluate : 6.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1224 random chunks: chunk 595 optimal weight: 6.9990 chunk 771 optimal weight: 20.0000 chunk 1034 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 chunk 895 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 269 optimal weight: 9.9990 chunk 972 optimal weight: 9.9990 chunk 407 optimal weight: 6.9990 chunk 998 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN A 215 ASN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 GLN N 156 HIS ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 188 ASN ** R 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 50 ASN ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 ASN ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 27 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 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 63 ASN ** z 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.109268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.092961 restraints weight = 803678.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.094323 restraints weight = 963308.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.095378 restraints weight = 587752.177| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.8980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.151 163182 Z= 0.399 Angle : 0.956 19.254 239544 Z= 0.477 Chirality : 0.048 0.371 29845 Planarity : 0.008 0.171 15619 Dihedral : 26.181 179.780 72307 Min Nonbonded Distance : 0.952 Molprobity Statistics. All-atom Clashscore : 43.92 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.60 % Favored : 87.93 % Rotamer: Outliers : 0.04 % Allowed : 0.71 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.04 % Twisted Proline : 1.48 % 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: -2.52 (0.09), residues: 8147 helix: -0.93 (0.08), residues: 3179 sheet: -1.59 (0.17), residues: 774 loop : -2.31 (0.09), residues: 4194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP x 193 HIS 0.028 0.003 HIS 5 267 PHE 0.057 0.004 PHE 4 10 TYR 0.069 0.004 TYR 5 398 ARG 0.036 0.001 ARG r 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47377.59 seconds wall clock time: 825 minutes 22.17 seconds (49522.17 seconds total)