Starting phenix.real_space_refine on Wed Mar 20 17:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t59_10380/03_2024/6t59_10380_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t59_10380/03_2024/6t59_10380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t59_10380/03_2024/6t59_10380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t59_10380/03_2024/6t59_10380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t59_10380/03_2024/6t59_10380_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t59_10380/03_2024/6t59_10380_neut.pdb" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 53 atoms to isotropic. 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 3887 5.49 5 Mg 220 5.21 5 S 265 5.16 5 C 74715 2.51 5 N 26802 2.21 5 O 37153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A3 GLU 36": "OE1" <-> "OE2" Residue "A3 GLU 80": "OE1" <-> "OE2" Residue "A3 GLU 118": "OE1" <-> "OE2" Residue "A3 GLU 142": "OE1" <-> "OE2" Residue "A3 GLU 208": "OE1" <-> "OE2" Residue "A3 ARG 242": "NH1" <-> "NH2" Residue "B3 ARG 10": "NH1" <-> "NH2" Residue "B3 PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 71": "OE1" <-> "OE2" Residue "B3 GLU 113": "OE1" <-> "OE2" Residue "B3 GLU 199": "OE1" <-> "OE2" Residue "B3 GLU 202": "OE1" <-> "OE2" Residue "B3 ARG 268": "NH1" <-> "NH2" Residue "B3 GLU 279": "OE1" <-> "OE2" Residue "B3 GLU 383": "OE1" <-> "OE2" Residue "C3 ARG 5": "NH1" <-> "NH2" Residue "C3 ARG 49": "NH1" <-> "NH2" Residue "C3 GLU 56": "OE1" <-> "OE2" Residue "C3 GLU 149": "OE1" <-> "OE2" Residue "C3 GLU 297": "OE1" <-> "OE2" Residue "C3 ARG 306": "NH1" <-> "NH2" Residue "C3 ARG 323": "NH1" <-> "NH2" Residue "C3 ARG 337": "NH1" <-> "NH2" Residue "C3 GLU 352": "OE1" <-> "OE2" Residue "D3 ARG 15": "NH1" <-> "NH2" Residue "D3 ARG 23": "NH1" <-> "NH2" Residue "D3 ARG 24": "NH1" <-> "NH2" Residue "D3 ARG 33": "NH1" <-> "NH2" Residue "D3 ARG 50": "NH1" <-> "NH2" Residue "D3 GLU 82": "OE1" <-> "OE2" Residue "D3 ARG 108": "NH1" <-> "NH2" Residue "D3 GLU 133": "OE1" <-> "OE2" Residue "D3 ARG 179": "NH1" <-> "NH2" Residue "D3 GLU 186": "OE1" <-> "OE2" Residue "D3 GLU 214": "OE1" <-> "OE2" Residue "D3 GLU 216": "OE1" <-> "OE2" Residue "D3 ARG 259": "NH1" <-> "NH2" Residue "E3 ARG 61": "NH1" <-> "NH2" Residue "E3 GLU 122": "OE1" <-> "OE2" Residue "E3 ARG 126": "NH1" <-> "NH2" Residue "E3 ARG 164": "NH1" <-> "NH2" Residue "E3 ARG 191": "NH1" <-> "NH2" Residue "E3 GLU 247": "OE1" <-> "OE2" Residue "F3 ARG 45": "NH1" <-> "NH2" Residue "F3 GLU 67": "OE1" <-> "OE2" Residue "F3 GLU 85": "OE1" <-> "OE2" Residue "F3 ARG 93": "NH1" <-> "NH2" Residue "F3 GLU 151": "OE1" <-> "OE2" Residue "F3 ARG 156": "NH1" <-> "NH2" Residue "F3 ARG 235": "NH1" <-> "NH2" Residue "F3 GLU 236": "OE1" <-> "OE2" Residue "F3 ARG 244": "NH1" <-> "NH2" Residue "G3 ARG 142": "NH1" <-> "NH2" Residue "G3 ARG 166": "NH1" <-> "NH2" Residue "G3 GLU 201": "OE1" <-> "OE2" Residue "G3 GLU 218": "OE1" <-> "OE2" Residue "G3 ARG 242": "NH1" <-> "NH2" Residue "G3 GLU 273": "OE1" <-> "OE2" Residue "G3 ARG 287": "NH1" <-> "NH2" Residue "G3 GLU 313": "OE1" <-> "OE2" Residue "H3 ARG 23": "NH1" <-> "NH2" Residue "H3 GLU 44": "OE1" <-> "OE2" Residue "H3 GLU 66": "OE1" <-> "OE2" Residue "H3 ARG 89": "NH1" <-> "NH2" Residue "H3 ARG 127": "NH1" <-> "NH2" Residue "H3 GLU 183": "OE1" <-> "OE2" Residue "I3 ARG 4": "NH1" <-> "NH2" Residue "I3 ARG 69": "NH1" <-> "NH2" Residue "I3 ARG 98": "NH1" <-> "NH2" Residue "I3 ARG 116": "NH1" <-> "NH2" Residue "I3 GLU 146": "OE1" <-> "OE2" Residue "I3 ARG 153": "NH1" <-> "NH2" Residue "I3 ARG 162": "NH1" <-> "NH2" Residue "I3 GLU 180": "OE1" <-> "OE2" Residue "I3 GLU 182": "OE1" <-> "OE2" Residue "I3 ARG 203": "NH1" <-> "NH2" Residue "I3 ARG 210": "NH1" <-> "NH2" Residue "J3 GLU 28": "OE1" <-> "OE2" Residue "J3 ARG 35": "NH1" <-> "NH2" Residue "J3 ARG 64": "NH1" <-> "NH2" Residue "J3 GLU 81": "OE1" <-> "OE2" Residue "J3 GLU 93": "OE1" <-> "OE2" Residue "J3 ARG 146": "NH1" <-> "NH2" Residue "J3 ARG 164": "NH1" <-> "NH2" Residue "L3 ARG 31": "NH1" <-> "NH2" Residue "L3 ARG 49": "NH1" <-> "NH2" Residue "L3 ARG 65": "NH1" <-> "NH2" Residue "L3 ARG 102": "NH1" <-> "NH2" Residue "L3 GLU 108": "OE1" <-> "OE2" Residue "L3 ARG 116": "NH1" <-> "NH2" Residue "L3 GLU 142": "OE1" <-> "OE2" Residue "L3 ARG 158": "NH1" <-> "NH2" Residue "L3 GLU 171": "OE1" <-> "OE2" Residue "L3 GLU 172": "OE1" <-> "OE2" Residue "L3 GLU 204": "OE1" <-> "OE2" Residue "M3 ARG 11": "NH1" <-> "NH2" Residue "M3 ARG 98": "NH1" <-> "NH2" Residue "M3 ARG 109": "NH1" <-> "NH2" Residue "M3 ARG 119": "NH1" <-> "NH2" Residue "M3 ARG 121": "NH1" <-> "NH2" Residue "M3 GLU 126": "OE1" <-> "OE2" Residue "N3 GLU 9": "OE1" <-> "OE2" Residue "N3 ARG 24": "NH1" <-> "NH2" Residue "N3 ARG 50": "NH1" <-> "NH2" Residue "N3 ARG 65": "NH1" <-> "NH2" Residue "N3 ARG 96": "NH1" <-> "NH2" Residue "N3 GLU 103": "OE1" <-> "OE2" Residue "N3 GLU 104": "OE1" <-> "OE2" Residue "N3 ARG 169": "NH1" <-> "NH2" Residue "N3 ARG 189": "NH1" <-> "NH2" Residue "N3 ARG 194": "NH1" <-> "NH2" Residue "O3 ARG 78": "NH1" <-> "NH2" Residue "O3 ARG 128": "NH1" <-> "NH2" Residue "O3 ARG 140": "NH1" <-> "NH2" Residue "O3 GLU 157": "OE1" <-> "OE2" Residue "O3 GLU 162": "OE1" <-> "OE2" Residue "P3 ARG 3": "NH1" <-> "NH2" Residue "P3 GLU 9": "OE1" <-> "OE2" Residue "P3 GLU 31": "OE1" <-> "OE2" Residue "P3 ARG 62": "NH1" <-> "NH2" Residue "P3 GLU 154": "OE1" <-> "OE2" Residue "Q3 GLU 17": "OE1" <-> "OE2" Residue "Q3 ARG 37": "NH1" <-> "NH2" Residue "Q3 ARG 55": "NH1" <-> "NH2" Residue "Q3 GLU 76": "OE1" <-> "OE2" Residue "Q3 ARG 91": "NH1" <-> "NH2" Residue "Q3 GLU 94": "OE1" <-> "OE2" Residue "Q3 ARG 134": "NH1" <-> "NH2" Residue "Q3 GLU 147": "OE1" <-> "OE2" Residue "Q3 ARG 180": "NH1" <-> "NH2" Residue "Q3 ARG 181": "NH1" <-> "NH2" Residue "R3 GLU 28": "OE1" <-> "OE2" Residue "R3 GLU 31": "OE1" <-> "OE2" Residue "R3 ARG 38": "NH1" <-> "NH2" Residue "R3 ARG 42": "NH1" <-> "NH2" Residue "R3 ARG 74": "NH1" <-> "NH2" Residue "R3 GLU 111": "OE1" <-> "OE2" Residue "R3 ARG 117": "NH1" <-> "NH2" Residue "R3 GLU 140": "OE1" <-> "OE2" Residue "S3 ARG 31": "NH1" <-> "NH2" Residue "S3 ARG 43": "NH1" <-> "NH2" Residue "S3 GLU 60": "OE1" <-> "OE2" Residue "S3 GLU 69": "OE1" <-> "OE2" Residue "S3 ARG 83": "NH1" <-> "NH2" Residue "S3 ARG 111": "NH1" <-> "NH2" Residue "S3 ARG 118": "NH1" <-> "NH2" Residue "S3 GLU 131": "OE1" <-> "OE2" Residue "S3 ARG 139": "NH1" <-> "NH2" Residue "S3 ARG 161": "NH1" <-> "NH2" Residue "S3 ARG 166": "NH1" <-> "NH2" Residue "T3 GLU 111": "OE1" <-> "OE2" Residue "T3 GLU 118": "OE1" <-> "OE2" Residue "T3 GLU 121": "OE1" <-> "OE2" Residue "T3 ARG 130": "NH1" <-> "NH2" Residue "T3 GLU 152": "OE1" <-> "OE2" Residue "T3 GLU 157": "OE1" <-> "OE2" Residue "U3 GLU 40": "OE1" <-> "OE2" Residue "U3 ARG 65": "NH1" <-> "NH2" Residue "U3 GLU 108": "OE1" <-> "OE2" Residue "V3 ARG 48": "NH1" <-> "NH2" Residue "V3 ARG 51": "NH1" <-> "NH2" Residue "V3 ARG 85": "NH1" <-> "NH2" Residue "V3 ARG 89": "NH1" <-> "NH2" Residue "V3 GLU 99": "OE1" <-> "OE2" Residue "V3 GLU 111": "OE1" <-> "OE2" Residue "V3 ARG 131": "NH1" <-> "NH2" Residue "W3 GLU 4": "OE1" <-> "OE2" Residue "W3 ARG 19": "NH1" <-> "NH2" Residue "X3 ARG 53": "NH1" <-> "NH2" Residue "X3 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X3 GLU 84": "OE1" <-> "OE2" Residue "X3 ARG 129": "NH1" <-> "NH2" Residue "X3 ARG 139": "NH1" <-> "NH2" Residue "Y3 ARG 27": "NH1" <-> "NH2" Residue "Y3 GLU 37": "OE1" <-> "OE2" Residue "Y3 ARG 87": "NH1" <-> "NH2" Residue "Y3 GLU 88": "OE1" <-> "OE2" Residue "Y3 GLU 120": "OE1" <-> "OE2" Residue "Z3 ARG 65": "NH1" <-> "NH2" Residue "Z3 GLU 113": "OE1" <-> "OE2" Residue "Z3 GLU 120": "OE1" <-> "OE2" Residue "a3 ARG 4": "NH1" <-> "NH2" Residue "a3 ARG 9": "NH1" <-> "NH2" Residue "a3 ARG 21": "NH1" <-> "NH2" Residue "a3 ARG 65": "NH1" <-> "NH2" Residue "a3 GLU 84": "OE1" <-> "OE2" Residue "a3 ARG 105": "NH1" <-> "NH2" Residue "a3 GLU 134": "OE1" <-> "OE2" Residue "a3 GLU 135": "OE1" <-> "OE2" Residue "b3 ARG 14": "NH1" <-> "NH2" Residue "b3 ARG 18": "NH1" <-> "NH2" Residue "b3 ARG 25": "NH1" <-> "NH2" Residue "b3 ARG 28": "NH1" <-> "NH2" Residue "b3 GLU 30": "OE1" <-> "OE2" Residue "b3 GLU 70": "OE1" <-> "OE2" Residue "b3 ARG 95": "NH1" <-> "NH2" Residue "b3 ARG 109": "NH1" <-> "NH2" Residue "b3 ARG 111": "NH1" <-> "NH2" Residue "c3 ARG 39": "NH1" <-> "NH2" Residue "c3 GLU 59": "OE1" <-> "OE2" Residue "c3 GLU 61": "OE1" <-> "OE2" Residue "c3 GLU 80": "OE1" <-> "OE2" Residue "d3 GLU 24": "OE1" <-> "OE2" Residue "d3 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d3 GLU 48": "OE1" <-> "OE2" Residue "d3 GLU 56": "OE1" <-> "OE2" Residue "d3 ARG 90": "NH1" <-> "NH2" Residue "e3 ARG 36": "NH1" <-> "NH2" Residue "e3 ARG 39": "NH1" <-> "NH2" Residue "e3 GLU 84": "OE1" <-> "OE2" Residue "e3 GLU 98": "OE1" <-> "OE2" Residue "e3 ARG 108": "NH1" <-> "NH2" Residue "e3 GLU 113": "OE1" <-> "OE2" Residue "e3 ARG 128": "NH1" <-> "NH2" Residue "f3 GLU 31": "OE1" <-> "OE2" Residue "f3 GLU 38": "OE1" <-> "OE2" Residue "f3 ARG 89": "NH1" <-> "NH2" Residue "g3 ARG 29": "NH1" <-> "NH2" Residue "g3 ARG 60": "NH1" <-> "NH2" Residue "h3 GLU 15": "OE1" <-> "OE2" Residue "h3 GLU 16": "OE1" <-> "OE2" Residue "h3 GLU 27": "OE1" <-> "OE2" Residue "h3 ARG 48": "NH1" <-> "NH2" Residue "h3 ARG 94": "NH1" <-> "NH2" Residue "h3 GLU 111": "OE1" <-> "OE2" Residue "i3 ARG 4": "NH1" <-> "NH2" Residue "i3 GLU 46": "OE1" <-> "OE2" Residue "i3 ARG 68": "NH1" <-> "NH2" Residue "i3 ARG 76": "NH1" <-> "NH2" Residue "j3 ARG 11": "NH1" <-> "NH2" Residue "j3 ARG 20": "NH1" <-> "NH2" Residue "j3 ARG 45": "NH1" <-> "NH2" Residue "j3 ARG 55": "NH1" <-> "NH2" Residue "j3 ARG 56": "NH1" <-> "NH2" Residue "j3 ARG 72": "NH1" <-> "NH2" Residue "j3 ARG 79": "NH1" <-> "NH2" Residue "k3 ARG 3": "NH1" <-> "NH2" Residue "k3 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k3 GLU 51": "OE1" <-> "OE2" Residue "k3 GLU 68": "OE1" <-> "OE2" Residue "l3 ARG 8": "NH1" <-> "NH2" Residue "l3 ARG 21": "NH1" <-> "NH2" Residue "l3 ARG 36": "NH1" <-> "NH2" Residue "m3 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m3 ARG 71": "NH1" <-> "NH2" Residue "m3 ARG 85": "NH1" <-> "NH2" Residue "n3 ARG 2": "NH1" <-> "NH2" Residue "n3 ARG 9": "NH1" <-> "NH2" Residue "n3 ARG 15": "NH1" <-> "NH2" Residue "n3 ARG 23": "NH1" <-> "NH2" Residue "o3 ARG 40": "NH1" <-> "NH2" Residue "o3 ARG 43": "NH1" <-> "NH2" Residue "o3 ARG 69": "NH1" <-> "NH2" Residue "o3 GLU 74": "OE1" <-> "OE2" Residue "o3 ARG 78": "NH1" <-> "NH2" Residue "o3 GLU 92": "OE1" <-> "OE2" Residue "p3 ARG 17": "NH1" <-> "NH2" Residue "p3 ARG 49": "NH1" <-> "NH2" Residue "p3 ARG 84": "NH1" <-> "NH2" Residue "p3 GLU 88": "OE1" <-> "OE2" Residue "r3 ARG 35": "NH1" <-> "NH2" Residue "r3 ARG 39": "NH1" <-> "NH2" Residue "r3 GLU 52": "OE1" <-> "OE2" Residue "r3 ARG 71": "NH1" <-> "NH2" Residue "r3 ARG 107": "NH1" <-> "NH2" Residue "r3 ARG 112": "NH1" <-> "NH2" Residue "r3 ARG 113": "NH1" <-> "NH2" Residue "s3 GLU 70": "OE1" <-> "OE2" Residue "s3 GLU 93": "OE1" <-> "OE2" Residue "s3 GLU 120": "OE1" <-> "OE2" Residue "s3 GLU 153": "OE1" <-> "OE2" Residue "t3 ARG 16": "NH1" <-> "NH2" Residue "t3 ARG 57": "NH1" <-> "NH2" Residue "t3 GLU 87": "OE1" <-> "OE2" Residue "TT GLU 139": "OE1" <-> "OE2" Residue "TT GLU 150": "OE1" <-> "OE2" Residue "TT GLU 160": "OE1" <-> "OE2" Residue "TT ARG 183": "NH1" <-> "NH2" Residue "TT ARG 199": "NH1" <-> "NH2" Residue "TT GLU 203": "OE1" <-> "OE2" Residue "TT GLU 205": "OE1" <-> "OE2" Residue "TT ARG 267": "NH1" <-> "NH2" Residue "TT GLU 286": "OE1" <-> "OE2" Residue "TT ARG 298": "NH1" <-> "NH2" Residue "TT GLU 308": "OE1" <-> "OE2" Residue "TT ARG 310": "NH1" <-> "NH2" Residue "TT GLU 318": "OE1" <-> "OE2" Residue "TT ARG 346": "NH1" <-> "NH2" Residue "TT TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TT ARG 444": "NH1" <-> "NH2" Residue "TT GLU 460": "OE1" <-> "OE2" Residue "1 ARG 2": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143047 Number of models: 1 Model: "" Number of chains: 64 Chain: "A3" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 14, 'TRANS': 233} Chain: "B3" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3172 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "C3" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D3" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2391 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "E3" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain breaks: 3 Chain: "F3" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1875 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "G3" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1879 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain breaks: 1 Chain: "H3" 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: "I3" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1664 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "J3" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1362 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "L3" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1702 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M3" 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: "N3" 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: "O3" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1630 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "P3" 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: "Q3" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1514 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R3" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1294 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "S3" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1462 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "T3" 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: "U3" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "V3" 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: "W3" 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: "X3" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "Y3" 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: "Z3" 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: "a3" 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: "b3" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Chain: "c3" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 761 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "d3" 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: "e3" 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: "f3" 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: "g3" 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: "h3" 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: "i3" 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: "j3" 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: "k3" 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: "l3" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 447 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m3" 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: "n3" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "o3" 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: "p3" 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: "r3" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "s3" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "t3" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1160 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "23" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1616 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 34} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain breaks: 1 Chain: "54" Number of atoms: 75972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3543, 75972 Classifications: {'RNA': 3543} Modifications used: {'rna2p_pur': 356, 'rna2p_pyr': 215, 'rna3p_pur': 1590, 'rna3p_pyr': 1382} Link IDs: {'rna2p': 571, 'rna3p': 2971} Chain breaks: 27 Chain: "74" 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: "84" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3208 Classifications: {'RNA': 151} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 15, 'rna3p_pur': 59, 'rna3p_pyr': 63} Link IDs: {'rna2p': 28, 'rna3p': 122} Chain breaks: 1 Chain: "NI" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 150 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "NA" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "NB" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 55} Chain: "TT" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3337 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "1" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain breaks: 1 Chain: "P3" 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: "V3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g3" 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: "j3" 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: "m3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "54" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 201 Unusual residues: {' MG': 201} Classifications: {'undetermined': 201} Link IDs: {None: 200} Chain: "74" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "84" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 44833 SG CYSg3 46 98.769 167.437 209.748 1.00 63.15 S ATOM 44850 SG CYSg3 49 99.028 171.498 208.876 1.00 72.69 S ATOM 45113 SG CYSg3 83 101.005 170.935 211.638 1.00 54.01 S ATOM 47356 SG CYSj3 19 126.356 122.050 186.057 1.00 34.41 S ATOM 47384 SG CYSj3 22 127.820 119.998 183.479 1.00 37.79 S ATOM 47475 SG CYSj3 34 124.473 121.471 182.963 1.00 33.28 S ATOM 47494 SG CYSj3 37 125.130 118.737 185.247 1.00 34.82 S ATOM 49099 SG CYSm3 70 103.167 139.745 74.509 1.00 39.54 S ATOM 49125 SG CYSm3 73 106.080 140.836 75.987 1.00 38.69 S ATOM 49215 SG CYSm3 84 106.752 139.497 72.778 1.00 39.85 S ATOM 49259 SG CYSm3 89 106.189 137.383 75.596 1.00 37.34 S ATOM 49696 SG CYSo3 12 59.055 67.832 147.427 1.00 52.07 S ATOM 49720 SG CYSo3 15 57.418 64.154 148.126 1.00 54.98 S ATOM 50189 SG CYSo3 72 55.889 68.277 148.440 1.00 58.87 S ATOM 50226 SG CYSo3 77 58.560 66.460 150.467 1.00 66.04 S ATOM 50756 SG CYSp3 39 86.644 173.519 199.735 1.00 49.54 S ATOM 50779 SG CYSp3 42 88.214 176.040 201.429 1.00 54.29 S ATOM 50901 SG CYSp3 57 89.949 173.908 199.100 1.00 51.29 S Time building chain proxies: 53.16, per 1000 atoms: 0.37 Number of scatterers: 143047 At special positions: 0 Unit cell: (236.74, 235.41, 277.97, 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 265 16.00 P 3887 15.00 Mg 220 11.99 O 37153 8.00 N 26802 7.00 C 74715 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.82 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNg3 201 " pdb="ZN ZNg3 201 " - pdb=" SG CYSg3 46 " pdb="ZN ZNg3 201 " - pdb=" SG CYSg3 49 " pdb="ZN ZNg3 201 " - pdb=" SG CYSg3 83 " pdb=" ZNj3 101 " pdb="ZN ZNj3 101 " - pdb=" SG CYSj3 37 " pdb="ZN ZNj3 101 " - pdb=" SG CYSj3 34 " pdb="ZN ZNj3 101 " - pdb=" SG CYSj3 22 " pdb="ZN ZNj3 101 " - pdb=" SG CYSj3 19 " pdb=" ZNm3 200 " pdb="ZN ZNm3 200 " - pdb=" SG CYSm3 73 " pdb="ZN ZNm3 200 " - pdb=" SG CYSm3 84 " pdb="ZN ZNm3 200 " - pdb=" SG CYSm3 70 " pdb="ZN ZNm3 200 " - pdb=" SG CYSm3 89 " pdb=" ZNo3 200 " pdb="ZN ZNo3 200 " - pdb=" SG CYSo3 15 " pdb="ZN ZNo3 200 " - pdb=" SG CYSo3 12 " pdb="ZN ZNo3 200 " - pdb=" SG CYSo3 72 " pdb="ZN ZNo3 200 " - pdb=" SG CYSo3 77 " pdb=" ZNp3 100 " pdb="ZN ZNp3 100 " - pdb=" SG CYSp3 39 " pdb="ZN ZNp3 100 " - pdb=" SG CYSp3 42 " pdb="ZN ZNp3 100 " - pdb=" SG CYSp3 57 " Number of angles added : 18 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13762 Finding SS restraints... Secondary structure from input PDB file: 272 helices and 85 sheets defined 36.9% alpha, 12.6% beta 1065 base pairs and 2111 stacking pairs defined. Time for finding SS restraints: 49.02 Creating SS restraints... Processing helix chain 'A3' and resid 7 through 11 removed outlier: 3.514A pdb=" N LYSA3 10 " --> pdb=" O GLYA3 7 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYA3 11 " --> pdb=" O GLNA3 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A3' and resid 7 through 11' Processing helix chain 'A3' and resid 33 through 39 Processing helix chain 'A3' and resid 173 through 177 removed outlier: 3.820A pdb=" N LYSA3 177 " --> pdb=" O ARGA3 174 " (cutoff:3.500A) Processing helix chain 'A3' and resid 181 through 190 removed outlier: 3.680A pdb=" N ALAA3 185 " --> pdb=" O LYSA3 181 " (cutoff:3.500A) Processing helix chain 'A3' and resid 200 through 204 Processing helix chain 'B3' and resid 111 through 117 removed outlier: 3.711A pdb=" N ARGB3 117 " --> pdb=" O GLUB3 113 " (cutoff:3.500A) Processing helix chain 'B3' and resid 133 through 137 Processing helix chain 'B3' and resid 139 through 156 removed outlier: 3.851A pdb=" N GLNB3 145 " --> pdb=" O ALAB3 141 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N METB3 153 " --> pdb=" O ASPB3 149 " (cutoff:3.500A) Processing helix chain 'B3' and resid 167 through 171 removed outlier: 3.626A pdb=" N LEUB3 170 " --> pdb=" O GLNB3 167 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEUB3 171 " --> pdb=" O METB3 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 167 through 171' Processing helix chain 'B3' and resid 189 through 198 removed outlier: 3.527A pdb=" N ASPB3 195 " --> pdb=" O ALAB3 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRPB3 196 " --> pdb=" O GLUB3 192 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALAB3 197 " --> pdb=" O LYSB3 193 " (cutoff:3.500A) Processing helix chain 'B3' and resid 199 through 201 No H-bonds generated for 'chain 'B3' and resid 199 through 201' Processing helix chain 'B3' and resid 206 through 210 Processing helix chain 'B3' and resid 230 through 235 Processing helix chain 'B3' and resid 381 through 390 Processing helix chain 'C3' and resid 25 through 30 Processing helix chain 'C3' and resid 33 through 45 removed outlier: 3.614A pdb=" N ASNC3 43 " --> pdb=" O PHEC3 39 " (cutoff:3.500A) Processing helix chain 'C3' and resid 116 through 129 removed outlier: 3.516A pdb=" N TYRC3 122 " --> pdb=" O THRC3 118 " (cutoff:3.500A) Processing helix chain 'C3' and resid 133 through 139 Processing helix chain 'C3' and resid 155 through 161 removed outlier: 3.614A pdb=" N VALC3 158 " --> pdb=" O GLUC3 155 " (cutoff:3.500A) Processing helix chain 'C3' and resid 163 through 174 removed outlier: 3.526A pdb=" N ALAC3 167 " --> pdb=" O LYSC3 163 " (cutoff:3.500A) Processing helix chain 'C3' and resid 176 through 185 removed outlier: 3.652A pdb=" N ILEC3 180 " --> pdb=" O ALAC3 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYSC3 182 " --> pdb=" O ASNC3 178 " (cutoff:3.500A) Processing helix chain 'C3' and resid 192 through 198 removed outlier: 4.024A pdb=" N ASNC3 198 " --> pdb=" O LYSC3 195 " (cutoff:3.500A) Processing helix chain 'C3' and resid 216 through 222 Processing helix chain 'C3' and resid 233 through 235 No H-bonds generated for 'chain 'C3' and resid 233 through 235' Processing helix chain 'C3' and resid 236 through 241 Processing helix chain 'C3' and resid 242 through 245 removed outlier: 3.687A pdb=" N HISC3 245 " --> pdb=" O PROC3 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C3' and resid 242 through 245' Processing helix chain 'C3' and resid 254 through 258 Processing helix chain 'C3' and resid 259 through 264 Processing helix chain 'C3' and resid 288 through 294 Processing helix chain 'C3' and resid 295 through 300 removed outlier: 3.635A pdb=" N ARGC3 300 " --> pdb=" O PROC3 296 " (cutoff:3.500A) Processing helix chain 'C3' and resid 321 through 329 Processing helix chain 'C3' and resid 331 through 338 Processing helix chain 'C3' and resid 340 through 354 removed outlier: 3.533A pdb=" N VALC3 351 " --> pdb=" O HISC3 347 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLUC3 352 " --> pdb=" O LYSC3 348 " (cutoff:3.500A) Processing helix chain 'D3' and resid 9 through 15 removed outlier: 3.819A pdb=" N PHED3 13 " --> pdb=" O ASND3 9 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARGD3 15 " --> pdb=" O ALAD3 11 " (cutoff:3.500A) Processing helix chain 'D3' and resid 20 through 26 Processing helix chain 'D3' and resid 29 through 38 removed outlier: 4.319A pdb=" N ARGD3 35 " --> pdb=" O TYRD3 31 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VALD3 37 " --> pdb=" O ARGD3 33 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILED3 38 " --> pdb=" O LYSD3 34 " (cutoff:3.500A) Processing helix chain 'D3' and resid 40 through 44 Processing helix chain 'D3' and resid 82 through 87 removed outlier: 4.287A pdb=" N TYRD3 86 " --> pdb=" O GLUD3 82 " (cutoff:3.500A) Processing helix chain 'D3' and resid 94 through 114 removed outlier: 3.643A pdb=" N LEUD3 104 " --> pdb=" O CYSD3 100 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARGD3 112 " --> pdb=" O ARGD3 108 " (cutoff:3.500A) Processing helix chain 'D3' and resid 157 through 168 removed outlier: 3.972A pdb=" N LEUD3 163 " --> pdb=" O VALD3 159 " (cutoff:3.500A) Processing helix chain 'D3' and resid 191 through 200 removed outlier: 3.762A pdb=" N HISD3 195 " --> pdb=" O ASND3 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYSD3 197 " --> pdb=" O GLUD3 193 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HISD3 198 " --> pdb=" O VALD3 194 " (cutoff:3.500A) Processing helix chain 'D3' and resid 201 through 215 removed outlier: 3.878A pdb=" N ASPD3 206 " --> pdb=" O GLND3 202 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYRD3 207 " --> pdb=" O ASND3 203 " (cutoff:3.500A) Processing helix chain 'D3' and resid 215 through 223 Processing helix chain 'D3' and resid 223 through 229 removed outlier: 3.762A pdb=" N ILED3 227 " --> pdb=" O PHED3 223 " (cutoff:3.500A) Processing helix chain 'D3' and resid 232 through 234 No H-bonds generated for 'chain 'D3' and resid 232 through 234' Processing helix chain 'D3' and resid 235 through 250 removed outlier: 3.642A pdb=" N ASND3 250 " --> pdb=" O ALAD3 246 " (cutoff:3.500A) Processing helix chain 'D3' and resid 273 through 293 removed outlier: 3.522A pdb=" N VALD3 280 " --> pdb=" O LYSD3 276 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALAD3 281 " --> pdb=" O LYSD3 277 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYSD3 284 " --> pdb=" O VALD3 280 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARGD3 289 " --> pdb=" O ALAD3 285 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLND3 291 " --> pdb=" O PHED3 287 " (cutoff:3.500A) Processing helix chain 'E3' and resid 62 through 68 Processing helix chain 'E3' and resid 69 through 73 removed outlier: 3.613A pdb=" N LYSE3 72 " --> pdb=" O ALAE3 69 " (cutoff:3.500A) Processing helix chain 'E3' and resid 135 through 139 Processing helix chain 'E3' and resid 181 through 186 Processing helix chain 'E3' and resid 216 through 221 removed outlier: 3.550A pdb=" N PHEE3 220 " --> pdb=" O THRE3 216 " (cutoff:3.500A) Processing helix chain 'E3' and resid 247 through 265 removed outlier: 4.046A pdb=" N GLNE3 253 " --> pdb=" O ARGE3 249 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYSE3 254 " --> pdb=" O LYSE3 250 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASPE3 257 " --> pdb=" O GLNE3 253 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLNE3 259 " --> pdb=" O ALAE3 255 " (cutoff:3.500A) Proline residue: E3 262 - end of helix Processing helix chain 'E3' and resid 269 through 275 Processing helix chain 'F3' and resid 24 through 78 removed outlier: 3.589A pdb=" N ILEF3 29 " --> pdb=" O ALAF3 25 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYSF3 39 " --> pdb=" O LYSF3 35 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARGF3 42 " --> pdb=" O GLNF3 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYSF3 43 " --> pdb=" O LYSF3 39 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARGF3 45 " --> pdb=" O LEUF3 41 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HISF3 55 " --> pdb=" O GLUF3 51 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYSF3 58 " --> pdb=" O LYSF3 54 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLUF3 67 " --> pdb=" O METF3 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILEF3 68 " --> pdb=" O TYRF3 64 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALAF3 71 " --> pdb=" O GLUF3 67 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALAF3 74 " --> pdb=" O METF3 70 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALAF3 77 " --> pdb=" O METF3 73 " (cutoff:3.500A) Processing helix chain 'F3' and resid 101 through 111 removed outlier: 3.567A pdb=" N VALF3 107 " --> pdb=" O LYSF3 103 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLNF3 109 " --> pdb=" O ARGF3 105 " (cutoff:3.500A) Processing helix chain 'F3' and resid 125 through 130 Processing helix chain 'F3' and resid 135 through 138 Processing helix chain 'F3' and resid 145 through 156 removed outlier: 3.523A pdb=" N VALF3 149 " --> pdb=" O ASNF3 145 " (cutoff:3.500A) Processing helix chain 'F3' and resid 170 through 179 removed outlier: 4.013A pdb=" N ILEF3 174 " --> pdb=" O ASPF3 170 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARGF3 176 " --> pdb=" O THRF3 172 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SERF3 177 " --> pdb=" O LEUF3 173 " (cutoff:3.500A) Processing helix chain 'F3' and resid 180 through 182 No H-bonds generated for 'chain 'F3' and resid 180 through 182' Processing helix chain 'F3' and resid 185 through 195 Processing helix chain 'F3' and resid 199 through 207 removed outlier: 3.585A pdb=" N LEUF3 207 " --> pdb=" O ALAF3 203 " (cutoff:3.500A) Processing helix chain 'F3' and resid 225 through 229 Processing helix chain 'F3' and resid 238 through 245 removed outlier: 3.901A pdb=" N LEUF3 242 " --> pdb=" O GLNF3 238 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARGF3 245 " --> pdb=" O ARGF3 241 " (cutoff:3.500A) Processing helix chain 'G3' and resid 111 through 127 removed outlier: 4.070A pdb=" N ILEG3 122 " --> pdb=" O ARGG3 118 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEUG3 123 " --> pdb=" O GLNG3 119 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYRG3 124 " --> pdb=" O ARGG3 120 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYSG3 125 " --> pdb=" O ALAG3 121 " (cutoff:3.500A) Processing helix chain 'G3' and resid 130 through 135 Processing helix chain 'G3' and resid 141 through 152 removed outlier: 3.551A pdb=" N ALAG3 145 " --> pdb=" O ASPG3 141 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THRG3 146 " --> pdb=" O ARGG3 142 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLNG3 147 " --> pdb=" O GLNG3 143 " (cutoff:3.500A) Processing helix chain 'G3' and resid 160 through 176 removed outlier: 3.840A pdb=" N LYSG3 164 " --> pdb=" O LYSG3 160 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEUG3 167 " --> pdb=" O LYSG3 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALAG3 171 " --> pdb=" O LEUG3 167 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALAG3 176 " --> pdb=" O GLUG3 172 " (cutoff:3.500A) Processing helix chain 'G3' and resid 192 through 201 removed outlier: 3.817A pdb=" N THRG3 198 " --> pdb=" O ASNG3 194 " (cutoff:3.500A) Processing helix chain 'G3' and resid 216 through 220 Processing helix chain 'G3' and resid 222 through 231 removed outlier: 3.548A pdb=" N METG3 230 " --> pdb=" O LEUG3 226 " (cutoff:3.500A) Processing helix chain 'G3' and resid 242 through 247 removed outlier: 3.915A pdb=" N LEUG3 246 " --> pdb=" O ARGG3 242 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VALG3 247 " --> pdb=" O LEUG3 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'G3' and resid 242 through 247' Processing helix chain 'G3' and resid 264 through 277 removed outlier: 3.530A pdb=" N LEUG3 271 " --> pdb=" O ALAG3 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLUG3 273 " --> pdb=" O ALAG3 269 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALAG3 274 " --> pdb=" O LYSG3 270 " (cutoff:3.500A) Processing helix chain 'G3' and resid 282 through 287 Processing helix chain 'G3' and resid 296 through 318 removed outlier: 3.760A pdb=" N ARGG3 302 " --> pdb=" O LYSG3 298 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILEG3 303 " --> pdb=" O SERG3 299 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEUG3 306 " --> pdb=" O ARGG3 302 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEUG3 314 " --> pdb=" O LYSG3 310 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEUG3 318 " --> pdb=" O LEUG3 314 " (cutoff:3.500A) Processing helix chain 'H3' and resid 63 through 86 removed outlier: 3.541A pdb=" N ALAH3 68 " --> pdb=" O ARGH3 64 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THRH3 69 " --> pdb=" O LYSH3 65 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VALH3 70 " --> pdb=" O GLUH3 66 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARGH3 71 " --> pdb=" O LEUH3 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THRH3 72 " --> pdb=" O ALAH3 68 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILEH3 73 " --> pdb=" O THRH3 69 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLNH3 78 " --> pdb=" O CYSH3 74 " (cutoff:3.500A) Processing helix chain 'H3' and resid 107 through 109 No H-bonds generated for 'chain 'H3' and resid 107 through 109' Processing helix chain 'H3' and resid 116 through 120 Processing helix chain 'H3' and resid 150 through 164 Processing helix chain 'I3' and resid 42 through 46 removed outlier: 4.063A pdb=" N GLUI3 45 " --> pdb=" O LYSI3 42 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHEI3 46 " --> pdb=" O VALI3 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'I3' and resid 42 through 46' Processing helix chain 'I3' and resid 62 through 80 removed outlier: 3.566A pdb=" N CYSI3 71 " --> pdb=" O ALAI3 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYSI3 78 " --> pdb=" O LYSI3 74 " (cutoff:3.500A) Processing helix chain 'I3' and resid 144 through 155 removed outlier: 3.582A pdb=" N VALI3 148 " --> pdb=" O ASNI3 144 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALAI3 155 " --> pdb=" O ALAI3 151 " (cutoff:3.500A) Processing helix chain 'I3' and resid 156 through 159 removed outlier: 3.562A pdb=" N PHEI3 159 " --> pdb=" O LYSI3 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'I3' and resid 156 through 159' Processing helix chain 'I3' and resid 180 through 187 Processing helix chain 'I3' and resid 206 through 213 removed outlier: 4.185A pdb=" N ALAI3 211 " --> pdb=" O ASPI3 207 " (cutoff:3.500A) Processing helix chain 'J3' and resid 10 through 14 removed outlier: 3.589A pdb=" N GLUJ3 14 " --> pdb=" O PROJ3 11 " (cutoff:3.500A) Processing helix chain 'J3' and resid 30 through 44 removed outlier: 3.524A pdb=" N THRJ3 34 " --> pdb=" O GLYJ3 30 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEUJ3 40 " --> pdb=" O ALAJ3 36 " (cutoff:3.500A) Processing helix chain 'J3' and resid 77 through 88 removed outlier: 3.610A pdb=" N GLUJ3 81 " --> pdb=" O ALAJ3 77 " (cutoff:3.500A) Processing helix chain 'J3' and resid 111 through 116 removed outlier: 3.529A pdb=" N LEUJ3 115 " --> pdb=" O HISJ3 112 " (cutoff:3.500A) Processing helix chain 'J3' and resid 139 through 143 Processing helix chain 'J3' and resid 158 through 170 removed outlier: 4.553A pdb=" N ARGJ3 164 " --> pdb=" O GLUJ3 160 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRPJ3 165 " --> pdb=" O GLUJ3 161 " (cutoff:3.500A) Processing helix chain 'L3' and resid 27 through 46 removed outlier: 3.599A pdb=" N ILEL3 33 " --> pdb=" O PROL3 29 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARGL3 34 " --> pdb=" O ALAL3 30 " (cutoff:3.500A) Processing helix chain 'L3' and resid 77 through 85 Processing helix chain 'L3' and resid 90 through 94 Processing helix chain 'L3' and resid 109 through 119 Processing helix chain 'L3' and resid 140 through 145 removed outlier: 3.545A pdb=" N LEUL3 144 " --> pdb=" O SERL3 140 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYSL3 145 " --> pdb=" O ALAL3 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'L3' and resid 140 through 145' Processing helix chain 'L3' and resid 177 through 191 Processing helix chain 'L3' and resid 191 through 209 removed outlier: 3.649A pdb=" N ASPL3 206 " --> pdb=" O ALAL3 202 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VALL3 207 " --> pdb=" O ALAL3 203 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLUL3 208 " --> pdb=" O GLUL3 204 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYSL3 209 " --> pdb=" O GLNL3 205 " (cutoff:3.500A) Processing helix chain 'M3' and resid 69 through 81 removed outlier: 3.599A pdb=" N LYSM3 79 " --> pdb=" O LYSM3 75 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALAM3 80 " --> pdb=" O ALAM3 76 " (cutoff:3.500A) Processing helix chain 'M3' and resid 81 through 88 removed outlier: 3.648A pdb=" N ALAM3 87 " --> pdb=" O ASNM3 83 " (cutoff:3.500A) Processing helix chain 'M3' and resid 89 through 101 removed outlier: 3.539A pdb=" N LYSM3 94 " --> pdb=" O ARGM3 90 " (cutoff:3.500A) Processing helix chain 'M3' and resid 105 through 138 removed outlier: 3.511A pdb=" N TYRM3 110 " --> pdb=" O ASPM3 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLUM3 126 " --> pdb=" O ILEM3 122 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALAM3 138 " --> pdb=" O ALAM3 134 " (cutoff:3.500A) Processing helix chain 'N3' and resid 3 through 11 removed outlier: 3.540A pdb=" N GLUN3 9 " --> pdb=" O LYSN3 5 " (cutoff:3.500A) Processing helix chain 'N3' and resid 17 through 31 removed outlier: 3.772A pdb=" N ARGN3 24 " --> pdb=" O ARGN3 20 " (cutoff:3.500A) Processing helix chain 'N3' and resid 44 through 51 removed outlier: 3.530A pdb=" N LEUN3 51 " --> pdb=" O LYSN3 47 " (cutoff:3.500A) Processing helix chain 'N3' and resid 83 through 87 Processing helix chain 'N3' and resid 97 through 110 removed outlier: 3.519A pdb=" N GLUN3 104 " --> pdb=" O SERN3 100 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HISN3 109 " --> pdb=" O ARGN3 105 " (cutoff:3.500A) Processing helix chain 'N3' and resid 139 through 144 Processing helix chain 'N3' and resid 153 through 157 removed outlier: 3.581A pdb=" N LYSN3 157 " --> pdb=" O PRON3 154 " (cutoff:3.500A) Processing helix chain 'N3' and resid 165 through 170 Processing helix chain 'N3' and resid 180 through 184 removed outlier: 3.763A pdb=" N THRN3 183 " --> pdb=" O PHEN3 180 " (cutoff:3.500A) Processing helix chain 'N3' and resid 187 through 196 removed outlier: 3.510A pdb=" N TRPN3 192 " --> pdb=" O ARGN3 188 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARGN3 194 " --> pdb=" O ALAN3 190 " (cutoff:3.500A) Processing helix chain 'O3' and resid 15 through 27 removed outlier: 3.867A pdb=" N LYSO3 25 " --> pdb=" O ALAO3 21 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLNO3 26 " --> pdb=" O ILEO3 22 " (cutoff:3.500A) Processing helix chain 'O3' and resid 28 through 30 No H-bonds generated for 'chain 'O3' and resid 28 through 30' Processing helix chain 'O3' and resid 46 through 59 removed outlier: 3.561A pdb=" N PHEO3 57 " --> pdb=" O LYSO3 53 " (cutoff:3.500A) Processing helix chain 'O3' and resid 75 through 85 Processing helix chain 'O3' and resid 86 through 88 No H-bonds generated for 'chain 'O3' and resid 86 through 88' Processing helix chain 'O3' and resid 95 through 100 Processing helix chain 'O3' and resid 124 through 129 Processing helix chain 'O3' and resid 138 through 144 Processing helix chain 'O3' and resid 149 through 185 removed outlier: 3.796A pdb=" N THRO3 155 " --> pdb=" O ALAO3 151 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARGO3 160 " --> pdb=" O LEUO3 156 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYSO3 163 " --> pdb=" O LYSO3 159 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILEO3 166 " --> pdb=" O GLUO3 162 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HISO3 167 " --> pdb=" O LYSO3 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEUO3 174 " --> pdb=" O LYSO3 170 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARGO3 178 " --> pdb=" O LEUO3 174 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYSO3 183 " --> pdb=" O LYSO3 179 " (cutoff:3.500A) Processing helix chain 'O3' and resid 189 through 195 removed outlier: 3.883A pdb=" N ASPO3 194 " --> pdb=" O SERO3 190 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VALO3 195 " --> pdb=" O LYSO3 191 " (cutoff:3.500A) Processing helix chain 'P3' and resid 10 through 14 removed outlier: 3.880A pdb=" N SERP3 14 " --> pdb=" O PROP3 11 " (cutoff:3.500A) Processing helix chain 'P3' and resid 25 through 35 Processing helix chain 'P3' and resid 40 through 54 removed outlier: 3.711A pdb=" N THRP3 52 " --> pdb=" O LEUP3 48 " (cutoff:3.500A) Processing helix chain 'P3' and resid 85 through 103 removed outlier: 3.805A pdb=" N LEUP3 91 " --> pdb=" O SERP3 87 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEUP3 92 " --> pdb=" O ALAP3 88 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEUP3 95 " --> pdb=" O LEUP3 91 " (cutoff:3.500A) Processing helix chain 'P3' and resid 108 through 110 No H-bonds generated for 'chain 'P3' and resid 108 through 110' Processing helix chain 'P3' and resid 132 through 134 No H-bonds generated for 'chain 'P3' and resid 132 through 134' Processing helix chain 'Q3' and resid 27 through 39 removed outlier: 3.501A pdb=" N ARGQ3 37 " --> pdb=" O ARGQ3 33 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 43 through 52 removed outlier: 3.653A pdb=" N PHEQ3 52 " --> pdb=" O LEUQ3 48 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 63 through 71 Processing helix chain 'Q3' and resid 108 through 117 removed outlier: 4.047A pdb=" N ARGQ3 112 " --> pdb=" O ARGQ3 108 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 122 through 130 Processing helix chain 'Q3' and resid 146 through 151 Processing helix chain 'R3' and resid 6 through 15 Processing helix chain 'R3' and resid 28 through 33 removed outlier: 3.653A pdb=" N ILER3 32 " --> pdb=" O GLUR3 28 " (cutoff:3.500A) Processing helix chain 'R3' and resid 38 through 47 removed outlier: 3.981A pdb=" N LYSR3 43 " --> pdb=" O GLNR3 39 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEUR3 44 " --> pdb=" O GLNR3 40 " (cutoff:3.500A) Processing helix chain 'R3' and resid 60 through 71 removed outlier: 3.828A pdb=" N ALAR3 69 " --> pdb=" O LYSR3 65 " (cutoff:3.500A) Processing helix chain 'R3' and resid 84 through 89 Processing helix chain 'R3' and resid 90 through 112 removed outlier: 3.532A pdb=" N TRPR3 95 " --> pdb=" O GLUR3 91 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARGR3 107 " --> pdb=" O ARGR3 103 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SERR3 112 " --> pdb=" O ARGR3 108 " (cutoff:3.500A) Processing helix chain 'R3' and resid 116 through 129 removed outlier: 3.737A pdb=" N LEUR3 125 " --> pdb=" O HISR3 121 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYSR3 126 " --> pdb=" O SERR3 122 " (cutoff:3.500A) Processing helix chain 'R3' and resid 135 through 153 removed outlier: 3.708A pdb=" N HISR3 141 " --> pdb=" O ILER3 137 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARGR3 151 " --> pdb=" O ALAR3 147 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYSR3 152 " --> pdb=" O ASPR3 148 " (cutoff:3.500A) Processing helix chain 'S3' and resid 36 through 52 removed outlier: 3.613A pdb=" N SERS3 42 " --> pdb=" O VALS3 38 " (cutoff:3.500A) Processing helix chain 'S3' and resid 101 through 118 removed outlier: 3.539A pdb=" N ARGS3 111 " --> pdb=" O THRS3 107 " (cutoff:3.500A) Processing helix chain 'S3' and resid 139 through 144 removed outlier: 3.641A pdb=" N GLNS3 144 " --> pdb=" O PROS3 140 " (cutoff:3.500A) Processing helix chain 'T3' and resid 54 through 58 Processing helix chain 'T3' and resid 92 through 94 No H-bonds generated for 'chain 'T3' and resid 92 through 94' Processing helix chain 'T3' and resid 100 through 118 removed outlier: 4.167A pdb=" N SERT3 104 " --> pdb=" O LYST3 100 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHET3 105 " --> pdb=" O SERT3 101 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLUT3 111 " --> pdb=" O LYST3 107 " (cutoff:3.500A) Processing helix chain 'U3' and resid 25 through 30 removed outlier: 3.837A pdb=" N VALU3 29 " --> pdb=" O CYSU3 25 " (cutoff:3.500A) Processing helix chain 'U3' and resid 36 through 47 removed outlier: 4.012A pdb=" N PHEU3 42 " --> pdb=" O ASNU3 38 " (cutoff:3.500A) Processing helix chain 'U3' and resid 53 through 58 removed outlier: 3.664A pdb=" N LEUU3 56 " --> pdb=" O ALAU3 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLYU3 57 " --> pdb=" O GLYU3 54 " (cutoff:3.500A) Processing helix chain 'U3' and resid 80 through 94 removed outlier: 3.666A pdb=" N LYSU3 84 " --> pdb=" O LYSU3 80 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYSU3 93 " --> pdb=" O LYSU3 89 " (cutoff:3.500A) Processing helix chain 'V3' and resid 69 through 73 Processing helix chain 'V3' and resid 122 through 127 Processing helix chain 'V3' and resid 129 through 134 Processing helix chain 'W3' and resid 35 through 42 Processing helix chain 'W3' and resid 45 through 49 removed outlier: 3.841A pdb=" N ILEW3 49 " --> pdb=" O PROW3 46 " (cutoff:3.500A) Processing helix chain 'W3' and resid 52 through 59 removed outlier: 3.702A pdb=" N ARGW3 56 " --> pdb=" O THRW3 52 " (cutoff:3.500A) Processing helix chain 'X3' and resid 86 through 92 Processing helix chain 'X3' and resid 105 through 117 removed outlier: 4.202A pdb=" N LYSX3 115 " --> pdb=" O GLNX3 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEUX3 116 " --> pdb=" O ALAX3 112 " (cutoff:3.500A) Processing helix chain 'X3' and resid 145 through 154 removed outlier: 3.937A pdb=" N LYSX3 152 " --> pdb=" O ASPX3 148 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILEX3 153 " --> pdb=" O VALX3 149 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 10 through 20 removed outlier: 3.736A pdb=" N ASNY3 14 " --> pdb=" O ASPY3 10 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHEY3 19 " --> pdb=" O ARGY3 15 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 25 through 30 Processing helix chain 'Y3' and resid 35 through 43 removed outlier: 3.936A pdb=" N GLNY3 40 " --> pdb=" O LYSY3 36 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYSY3 41 " --> pdb=" O GLUY3 37 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 100 through 102 No H-bonds generated for 'chain 'Y3' and resid 100 through 102' Processing helix chain 'Y3' and resid 114 through 134 removed outlier: 3.521A pdb=" N LEUY3 119 " --> pdb=" O ARGY3 115 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLYY3 129 " --> pdb=" O SERY3 125 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLUY3 131 " --> pdb=" O GLNY3 127 " (cutoff:3.500A) Processing helix chain 'Z3' and resid 58 through 66 removed outlier: 3.760A pdb=" N ILEZ3 62 " --> pdb=" O GLYZ3 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALAZ3 63 " --> pdb=" O LYSZ3 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYSZ3 64 " --> pdb=" O LYSZ3 60 " (cutoff:3.500A) Processing helix chain 'Z3' and resid 97 through 102 removed outlier: 3.716A pdb=" N PHEZ3 101 " --> pdb=" O LYSZ3 98 " (cutoff:3.500A) Processing helix chain 'Z3' and resid 103 through 123 removed outlier: 3.730A pdb=" N LYSZ3 117 " --> pdb=" O GLUZ3 113 " (cutoff:3.500A) Processing helix chain 'Z3' and resid 127 through 132 removed outlier: 3.804A pdb=" N GLNZ3 132 " --> pdb=" O TRPZ3 129 " (cutoff:3.500A) Processing helix chain 'a3' and resid 2 through 6 Processing helix chain 'a3' and resid 41 through 48 Processing helix chain 'a3' and resid 76 through 81 removed outlier: 4.571A pdb=" N TRPa3 79 " --> pdb=" O ASPa3 76 " (cutoff:3.500A) Processing helix chain 'a3' and resid 83 through 88 removed outlier: 4.006A pdb=" N ARGa3 87 " --> pdb=" O SERa3 83 " (cutoff:3.500A) Processing helix chain 'a3' and resid 88 through 93 Processing helix chain 'a3' and resid 130 through 139 removed outlier: 3.631A pdb=" N ILEa3 137 " --> pdb=" O ALAa3 133 " (cutoff:3.500A) Processing helix chain 'b3' and resid 11 through 19 removed outlier: 4.367A pdb=" N HISb3 17 " --> pdb=" O SERb3 13 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARGb3 18 " --> pdb=" O ARGb3 14 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASNb3 19 " --> pdb=" O LYSb3 15 " (cutoff:3.500A) Processing helix chain 'b3' and resid 36 through 48 removed outlier: 3.750A pdb=" N ARGb3 44 " --> pdb=" O LEUb3 40 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHEb3 45 " --> pdb=" O ARGb3 41 " (cutoff:3.500A) Processing helix chain 'b3' and resid 49 through 54 Processing helix chain 'b3' and resid 57 through 76 removed outlier: 4.004A pdb=" N LYSb3 63 " --> pdb=" O ALAb3 59 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALAb3 69 " --> pdb=" O METb3 65 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLUb3 70 " --> pdb=" O ALAb3 66 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALAb3 74 " --> pdb=" O GLUb3 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEUb3 75 " --> pdb=" O ALAb3 71 " (cutoff:3.500A) Processing helix chain 'b3' and resid 90 through 100 removed outlier: 3.972A pdb=" N ALAb3 97 " --> pdb=" O LEUb3 93 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYRb3 98 " --> pdb=" O HISb3 94 " (cutoff:3.500A) Processing helix chain 'b3' and resid 105 through 114 removed outlier: 3.549A pdb=" N ILEb3 112 " --> pdb=" O ALAb3 108 " (cutoff:3.500A) Processing helix chain 'b3' and resid 115 through 117 No H-bonds generated for 'chain 'b3' and resid 115 through 117' Processing helix chain 'c3' and resid 11 through 22 removed outlier: 4.473A pdb=" N SERc3 16 " --> pdb=" O GLUc3 12 " (cutoff:3.500A) Processing helix chain 'c3' and resid 31 through 41 removed outlier: 3.527A pdb=" N LYSc3 36 " --> pdb=" O LYSc3 32 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N METc3 37 " --> pdb=" O GLNc3 33 " (cutoff:3.500A) Processing helix chain 'c3' and resid 55 through 67 removed outlier: 3.607A pdb=" N GLUc3 61 " --> pdb=" O LYSc3 57 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYRc3 62 " --> pdb=" O SERc3 58 " (cutoff:3.500A) Processing helix chain 'c3' and resid 77 through 85 removed outlier: 3.729A pdb=" N THRc3 83 " --> pdb=" O ILEc3 79 " (cutoff:3.500A) Processing helix chain 'c3' and resid 103 through 107 removed outlier: 3.699A pdb=" N SERc3 107 " --> pdb=" O ILEc3 104 " (cutoff:3.500A) Processing helix chain 'd3' and resid 28 through 33 Processing helix chain 'd3' and resid 37 through 39 No H-bonds generated for 'chain 'd3' and resid 37 through 39' Processing helix chain 'd3' and resid 40 through 57 removed outlier: 3.556A pdb=" N METd3 54 " --> pdb=" O ARGd3 50 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYSd3 55 " --> pdb=" O LYSd3 51 " (cutoff:3.500A) Processing helix chain 'd3' and resid 65 through 73 Processing helix chain 'e3' and resid 57 through 61 removed outlier: 3.807A pdb=" N TYRe3 60 " --> pdb=" O ASNe3 57 " (cutoff:3.500A) Processing helix chain 'e3' and resid 63 through 67 removed outlier: 3.674A pdb=" N LYSe3 67 " --> pdb=" O LYSe3 64 " (cutoff:3.500A) Processing helix chain 'e3' and resid 82 through 87 removed outlier: 4.123A pdb=" N GLUe3 86 " --> pdb=" O VALe3 82 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VALe3 87 " --> pdb=" O LYSe3 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'e3' and resid 82 through 87' Processing helix chain 'e3' and resid 104 through 118 removed outlier: 3.964A pdb=" N ALAe3 110 " --> pdb=" O LYSe3 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VALe3 112 " --> pdb=" O ARGe3 108 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARGe3 114 " --> pdb=" O ALAe3 110 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLNe3 117 " --> pdb=" O GLUe3 113 " (cutoff:3.500A) Processing helix chain 'f3' and resid 93 through 97 removed outlier: 3.627A pdb=" N ILEf3 97 " --> pdb=" O ALAf3 94 " (cutoff:3.500A) Processing helix chain 'g3' and resid 60 through 66 removed outlier: 3.827A pdb=" N METg3 65 " --> pdb=" O LYSg3 62 " (cutoff:3.500A) Processing helix chain 'g3' and resid 68 through 72 Processing helix chain 'g3' and resid 83 through 115 removed outlier: 3.580A pdb=" N ARGg3 90 " --> pdb=" O CYSg3 86 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARGg3 93 " --> pdb=" O ASPg3 89 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLUg3 98 " --> pdb=" O ALAg3 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEg3 102 " --> pdb=" O GLUg3 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALAg3 109 " --> pdb=" O LYSg3 105 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALAg3 111 " --> pdb=" O LEUg3 107 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLNg3 114 " --> pdb=" O GLNg3 110 " (cutoff:3.500A) Processing helix chain 'h3' and resid 6 through 10 removed outlier: 3.543A pdb=" N LEUh3 9 " --> pdb=" O ALAh3 6 " (cutoff:3.500A) Processing helix chain 'h3' and resid 13 through 38 removed outlier: 3.997A pdb=" N GLNh3 20 " --> pdb=" O GLUh3 16 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VALh3 26 " --> pdb=" O ASPh3 22 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALAh3 34 " --> pdb=" O GLNh3 30 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALh3 36 " --> pdb=" O ARGh3 32 " (cutoff:3.500A) Processing helix chain 'h3' and resid 40 through 45 Processing helix chain 'h3' and resid 46 through 73 removed outlier: 3.807A pdb=" N LYSh3 52 " --> pdb=" O ARGh3 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SERh3 53 " --> pdb=" O VALh3 49 " (cutoff:3.500A) Processing helix chain 'h3' and resid 88 through 93 removed outlier: 3.529A pdb=" N ARGh3 93 " --> pdb=" O ARGh3 89 " (cutoff:3.500A) Processing helix chain 'h3' and resid 96 through 101 Processing helix chain 'h3' and resid 106 through 114 removed outlier: 3.937A pdb=" N ARGh3 112 " --> pdb=" O GLNh3 108 " (cutoff:3.500A) Processing helix chain 'i3' and resid 36 through 46 Processing helix chain 'i3' and resid 53 through 63 removed outlier: 3.790A pdb=" N GLUi3 59 " --> pdb=" O ARGi3 55 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VALi3 63 " --> pdb=" O GLUi3 59 " (cutoff:3.500A) Processing helix chain 'i3' and resid 65 through 78 removed outlier: 3.714A pdb=" N ILEi3 73 " --> pdb=" O ALAi3 69 " (cutoff:3.500A) Processing helix chain 'i3' and resid 79 through 97 removed outlier: 3.716A pdb=" N GLUi3 89 " --> pdb=" O ARGi3 85 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEUi3 94 " --> pdb=" O LEUi3 90 " (cutoff:3.500A) Processing helix chain 'j3' and resid 5 through 9 Processing helix chain 'j3' and resid 50 through 56 removed outlier: 3.630A pdb=" N LYSj3 54 " --> pdb=" O SERj3 50 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARGj3 55 " --> pdb=" O ALAj3 51 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARGj3 56 " --> pdb=" O LYSj3 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'j3' and resid 50 through 56' Processing helix chain 'j3' and resid 66 through 74 removed outlier: 4.017A pdb=" N ARGj3 72 " --> pdb=" O LYSj3 68 " (cutoff:3.500A) Processing helix chain 'j3' and resid 75 through 77 No H-bonds generated for 'chain 'j3' and resid 75 through 77' Processing helix chain 'k3' and resid 8 through 16 removed outlier: 3.817A pdb=" N LEUk3 12 " --> pdb=" O ILEk3 8 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEUk3 13 " --> pdb=" O LYSk3 9 " (cutoff:3.500A) Processing helix chain 'k3' and resid 49 through 59 removed outlier: 3.614A pdb=" N GLUk3 54 " --> pdb=" O LYSk3 50 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYSk3 55 " --> pdb=" O GLUk3 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLNk3 58 " --> pdb=" O GLUk3 54 " (cutoff:3.500A) Processing helix chain 'l3' and resid 6 through 19 Processing helix chain 'l3' and resid 24 through 28 removed outlier: 3.767A pdb=" N TRPl3 28 " --> pdb=" O GLNl3 25 " (cutoff:3.500A) Processing helix chain 'm3' and resid 53 through 65 removed outlier: 3.577A pdb=" N LEUm3 59 " --> pdb=" O SERm3 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALAm3 60 " --> pdb=" O LEUm3 56 " (cutoff:3.500A) Processing helix chain 'n3' and resid 2 through 23 removed outlier: 3.626A pdb=" N LYSn3 8 " --> pdb=" O LYSn3 4 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARGn3 18 " --> pdb=" O LYSn3 14 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARGn3 23 " --> pdb=" O LYSn3 19 " (cutoff:3.500A) Processing helix chain 'o3' and resid 35 through 45 Processing helix chain 'p3' and resid 9 through 15 Processing helix chain 'p3' and resid 19 through 35 removed outlier: 3.855A pdb=" N LYSp3 28 " --> pdb=" O LYSp3 24 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILEp3 29 " --> pdb=" O METp3 25 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HISp3 34 " --> pdb=" O GLUp3 30 " (cutoff:3.500A) Processing helix chain 'p3' and resid 73 through 76 Processing helix chain 'p3' and resid 77 through 91 removed outlier: 3.503A pdb=" N ASPp3 91 " --> pdb=" O LYSp3 87 " (cutoff:3.500A) Processing helix chain 'r3' and resid 3 through 14 removed outlier: 3.627A pdb=" N VALr3 9 " --> pdb=" O LEUr3 5 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASNr3 12 " --> pdb=" O METr3 8 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N CYSr3 13 " --> pdb=" O VALr3 9 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SERr3 14 " --> pdb=" O VALr3 10 " (cutoff:3.500A) Processing helix chain 'r3' and resid 88 through 99 removed outlier: 4.148A pdb=" N ARGr3 94 " --> pdb=" O LEUr3 90 " (cutoff:3.500A) Processing helix chain 'r3' and resid 103 through 105 No H-bonds generated for 'chain 'r3' and resid 103 through 105' Processing helix chain 'r3' and resid 106 through 120 removed outlier: 3.629A pdb=" N ALAr3 116 " --> pdb=" O ARGr3 112 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEUr3 118 " --> pdb=" O ALAr3 114 " (cutoff:3.500A) Processing helix chain 's3' and resid 5 through 9 Processing helix chain 's3' and resid 10 through 19 removed outlier: 3.684A pdb=" N PHEs3 14 " --> pdb=" O LYSs3 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEUs3 15 " --> pdb=" O SERs3 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYSs3 16 " --> pdb=" O ASNs3 12 " (cutoff:3.500A) Processing helix chain 's3' and resid 36 through 41 Processing helix chain 's3' and resid 42 through 47 removed outlier: 4.431A pdb=" N SERs3 46 " --> pdb=" O GLNs3 42 " (cutoff:3.500A) Processing helix chain 's3' and resid 57 through 66 removed outlier: 3.782A pdb=" N LYSs3 63 " --> pdb=" O THRs3 59 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILEs3 65 " --> pdb=" O METs3 61 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARGs3 66 " --> pdb=" O ARGs3 62 " (cutoff:3.500A) Processing helix chain 's3' and resid 74 through 79 removed outlier: 4.466A pdb=" N LYSs3 77 " --> pdb=" O ALAs3 74 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEUs3 79 " --> pdb=" O GLUs3 76 " (cutoff:3.500A) Processing helix chain 's3' and resid 95 through 102 removed outlier: 3.527A pdb=" N ARGs3 99 " --> pdb=" O LEUs3 95 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEUs3 102 " --> pdb=" O ILEs3 98 " (cutoff:3.500A) Processing helix chain 's3' and resid 168 through 171 removed outlier: 4.063A pdb=" N GLUs3 171 " --> pdb=" O GLYs3 168 " (cutoff:3.500A) No H-bonds generated for 'chain 's3' and resid 168 through 171' Processing helix chain 's3' and resid 172 through 178 removed outlier: 3.817A pdb=" N LEUs3 178 " --> pdb=" O LEUs3 174 " (cutoff:3.500A) Processing helix chain 't3' and resid 28 through 33 removed outlier: 3.903A pdb=" N ILEt3 32 " --> pdb=" O LEUt3 28 " (cutoff:3.500A) Processing helix chain 't3' and resid 34 through 36 No H-bonds generated for 'chain 't3' and resid 34 through 36' Processing helix chain 't3' and resid 38 through 49 removed outlier: 4.070A pdb=" N ASPt3 45 " --> pdb=" O LYSt3 41 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALAt3 47 " --> pdb=" O GLYt3 43 " (cutoff:3.500A) Processing helix chain 't3' and resid 78 through 85 Processing helix chain 't3' and resid 109 through 120 removed outlier: 3.513A pdb=" N ALAt3 113 " --> pdb=" O ILEt3 109 " (cutoff:3.500A) Processing helix chain 't3' and resid 124 through 135 removed outlier: 3.843A pdb=" N ILEt3 132 " --> pdb=" O THRt3 128 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLYt3 134 " --> pdb=" O LYSt3 130 " (cutoff:3.500A) Processing helix chain 't3' and resid 136 through 140 removed outlier: 4.118A pdb=" N VALt3 139 " --> pdb=" O ALAt3 136 " (cutoff:3.500A) Processing helix chain 't3' and resid 146 through 151 removed outlier: 3.531A pdb=" N HISt3 149 " --> pdb=" O ARGt3 146 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILEt3 151 " --> pdb=" O PROt3 148 " (cutoff:3.500A) Processing helix chain 'NI' and resid 4 through 9 Processing helix chain 'NI' and resid 10 through 15 removed outlier: 3.852A pdb=" N ALANI 15 " --> pdb=" O ALANI 11 " (cutoff:3.500A) Processing helix chain 'NB' and resid 104 through 109 Processing helix chain 'TT' and resid 57 through 78 removed outlier: 3.510A pdb=" N LEUTT 68 " --> pdb=" O LYSTT 64 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VALTT 69 " --> pdb=" O LEUTT 65 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASPTT 70 " --> pdb=" O GLNTT 66 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEUTT 72 " --> pdb=" O LEUTT 68 " (cutoff:3.500A) Processing helix chain 'TT' and resid 78 through 83 removed outlier: 4.109A pdb=" N THRTT 82 " --> pdb=" O CYSTT 78 " (cutoff:3.500A) Processing helix chain 'TT' and resid 90 through 109 removed outlier: 4.231A pdb=" N METTT 99 " --> pdb=" O VALTT 95 " (cutoff:3.500A) Processing helix chain 'TT' and resid 116 through 127 removed outlier: 3.920A pdb=" N LEUTT 122 " --> pdb=" O GLNTT 118 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEUTT 127 " --> pdb=" O THRTT 123 " (cutoff:3.500A) Processing helix chain 'TT' and resid 128 through 130 No H-bonds generated for 'chain 'TT' and resid 128 through 130' Processing helix chain 'TT' and resid 134 through 148 removed outlier: 3.729A pdb=" N LYSTT 143 " --> pdb=" O GLUTT 139 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALATT 144 " --> pdb=" O LEUTT 140 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VALTT 145 " --> pdb=" O LEUTT 141 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYSTT 146 " --> pdb=" O SERTT 142 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEUTT 147 " --> pdb=" O LYSTT 143 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLUTT 148 " --> pdb=" O ALATT 144 " (cutoff:3.500A) Processing helix chain 'TT' and resid 153 through 162 Processing helix chain 'TT' and resid 167 through 182 removed outlier: 3.694A pdb=" N ALATT 171 " --> pdb=" O ASPTT 167 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SERTT 176 " --> pdb=" O HISTT 172 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALATT 178 " --> pdb=" O CYSTT 174 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEUTT 179 " --> pdb=" O PHETT 175 " (cutoff:3.500A) Processing helix chain 'TT' and resid 184 through 196 removed outlier: 4.199A pdb=" N SERTT 192 " --> pdb=" O LEUTT 188 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VALTT 194 " --> pdb=" O ASNTT 190 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARGTT 196 " --> pdb=" O SERTT 192 " (cutoff:3.500A) Processing helix chain 'TT' and resid 202 through 224 removed outlier: 3.706A pdb=" N METTT 211 " --> pdb=" O SERTT 207 " (cutoff:3.500A) Processing helix chain 'TT' and resid 227 through 245 removed outlier: 3.953A pdb=" N TRPTT 231 " --> pdb=" O ASPTT 227 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYTT 235 " --> pdb=" O TRPTT 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASNTT 236 " --> pdb=" O TYRTT 232 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SERTT 240 " --> pdb=" O ASNTT 236 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEUTT 241 " --> pdb=" O SERTT 237 " (cutoff:3.500A) Processing helix chain 'TT' and resid 248 through 257 removed outlier: 3.579A pdb=" N SERTT 252 " --> pdb=" O ASNTT 248 " (cutoff:3.500A) Processing helix chain 'TT' and resid 257 through 266 Processing helix chain 'TT' and resid 272 through 285 removed outlier: 4.120A pdb=" N HISTT 276 " --> pdb=" O ASNTT 272 " (cutoff:3.500A) Processing helix chain 'TT' and resid 288 through 303 removed outlier: 3.716A pdb=" N LEUTT 293 " --> pdb=" O TYRTT 289 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLUTT 294 " --> pdb=" O GLYTT 290 " (cutoff:3.500A) Processing helix chain 'TT' and resid 307 through 329 removed outlier: 3.695A pdb=" N GLUTT 313 " --> pdb=" O PROTT 309 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLNTT 314 " --> pdb=" O ARGTT 310 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASPTT 321 " --> pdb=" O LEUTT 317 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARGTT 322 " --> pdb=" O GLUTT 318 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEUTT 327 " --> pdb=" O LEUTT 323 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLUTT 328 " --> pdb=" O THRTT 324 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SERTT 329 " --> pdb=" O SERTT 325 " (cutoff:3.500A) Processing helix chain 'TT' and resid 330 through 333 removed outlier: 4.032A pdb=" N VALTT 333 " --> pdb=" O LYSTT 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'TT' and resid 330 through 333' Processing helix chain 'TT' and resid 334 through 343 removed outlier: 3.541A pdb=" N SERTT 340 " --> pdb=" O LYSTT 336 " (cutoff:3.500A) Processing helix chain 'TT' and resid 346 through 354 Proline residue: TT 352 - end of helix Processing helix chain 'TT' and resid 461 through 464 removed outlier: 3.501A pdb=" N LEUTT 464 " --> pdb=" O THRTT 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'TT' and resid 461 through 464' Processing helix chain 'TT' and resid 473 through 477 Processing sheet with id=AA1, first strand: chain 'A3' and resid 73 through 77 removed outlier: 6.182A pdb=" N LEUA3 58 " --> pdb=" O ILEA3 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILEA3 48 " --> pdb=" O LEUA3 58 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYSA3 60 " --> pdb=" O LYSA3 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A3' and resid 102 through 103 removed outlier: 3.788A pdb=" N LEUA3 102 " --> pdb=" O ALAA3 164 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THRA3 135 " --> pdb=" O LYSA3 149 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARGA3 147 " --> pdb=" O ILEA3 137 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N HISA3 139 " --> pdb=" O LYSA3 145 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYSA3 145 " --> pdb=" O HISA3 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A3' and resid 224 through 225 Processing sheet with id=AA4, first strand: chain 'B3' and resid 48 through 54 removed outlier: 5.821A pdb=" N LYSB3 50 " --> pdb=" O GLUB3 80 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLUB3 80 " --> pdb=" O LYSB3 50 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLYB3 52 " --> pdb=" O ILEB3 78 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHEB3 330 " --> pdb=" O ILEB3 287 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILEB3 287 " --> pdb=" O PHEB3 330 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N METB3 332 " --> pdb=" O TYRB3 285 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LYSB3 283 " --> pdb=" O LYSB3 334 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THRB3 278 " --> pdb=" O GLYB3 221 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLYB3 221 " --> pdb=" O THRB3 278 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ILEB3 280 " --> pdb=" O VALB3 219 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VALB3 219 " --> pdb=" O ILEB3 280 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VALB3 222 " --> pdb=" O VALB3 344 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VALB3 344 " --> pdb=" O VALB3 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B3' and resid 71 through 73 removed outlier: 6.616A pdb=" N VALB3 57 " --> pdb=" O LYSB3 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B3' and resid 98 through 106 removed outlier: 4.717A pdb=" N LEUB3 99 " --> pdb=" O THRB3 95 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THRB3 95 " --> pdb=" O LEUB3 99 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THRB3 101 " --> pdb=" O VALB3 93 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VALB3 93 " --> pdb=" O THRB3 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSB3 103 " --> pdb=" O GLYB3 91 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VALB3 86 " --> pdb=" O HISB3 165 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HISB3 165 " --> pdb=" O VALB3 86 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLYB3 88 " --> pdb=" O LEUB3 163 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILEB3 160 " --> pdb=" O VALB3 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B3' and resid 98 through 106 removed outlier: 4.717A pdb=" N LEUB3 99 " --> pdb=" O THRB3 95 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THRB3 95 " --> pdb=" O LEUB3 99 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THRB3 101 " --> pdb=" O VALB3 93 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VALB3 93 " --> pdb=" O THRB3 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSB3 103 " --> pdb=" O GLYB3 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B3' and resid 228 through 229 Processing sheet with id=AA9, first strand: chain 'B3' and resid 292 through 293 removed outlier: 3.606A pdb=" N LEUB3 292 " --> pdb=" O ILEB3 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C3' and resid 7 through 11 removed outlier: 5.184A pdb=" N LYSC3 20 " --> pdb=" O VALC3 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C3' and resid 64 through 66 removed outlier: 3.529A pdb=" N GLUC3 65 " --> pdb=" O ARGC3 78 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARGC3 78 " --> pdb=" O GLUC3 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C3' and resid 152 through 154 removed outlier: 6.754A pdb=" N LEUC3 152 " --> pdb=" O TRPC3 252 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRC3 253 " --> pdb=" O ILEC3 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C3' and resid 188 through 189 Processing sheet with id=AB5, first strand: chain 'D3' and resid 73 through 78 removed outlier: 3.577A pdb=" N TYRD3 66 " --> pdb=" O METD3 73 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILED3 64 " --> pdb=" O VALD3 75 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALAD3 77 " --> pdb=" O CYSD3 62 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYSD3 62 " --> pdb=" O ALAD3 77 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N METD3 51 " --> pdb=" O ASPD3 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E3' and resid 51 through 53 removed outlier: 7.161A pdb=" N ILEE3 56 " --> pdb=" O LEUE3 52 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E3' and resid 94 through 98 Processing sheet with id=AB8, first strand: chain 'E3' and resid 190 through 192 removed outlier: 6.730A pdb=" N LEUE3 177 " --> pdb=" O LEUE3 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F3' and resid 80 through 82 Processing sheet with id=AC1, first strand: chain 'F3' and resid 88 through 92 Processing sheet with id=AC2, first strand: chain 'F3' and resid 140 through 141 Processing sheet with id=AC3, first strand: chain 'F3' and resid 158 through 161 Processing sheet with id=AC4, first strand: chain 'G3' and resid 128 through 129 Processing sheet with id=AC5, first strand: chain 'G3' and resid 234 through 237 removed outlier: 6.198A pdb=" N VALG3 208 " --> pdb=" O CYSG3 235 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEUG3 237 " --> pdb=" O VALG3 208 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILEG3 210 " --> pdb=" O LEUG3 237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H3' and resid 3 through 11 removed outlier: 6.969A pdb=" N ILEH3 4 " --> pdb=" O TRPH3 61 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H3' and resid 17 through 20 removed outlier: 4.095A pdb=" N VALH3 25 " --> pdb=" O ARGH3 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H3' and resid 88 through 89 Processing sheet with id=AC9, first strand: chain 'H3' and resid 135 through 136 Processing sheet with id=AD1, first strand: chain 'H3' and resid 102 through 106 removed outlier: 3.672A pdb=" N LEUH3 111 " --> pdb=" O GLNH3 106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I3' and resid 35 through 37 removed outlier: 6.787A pdb=" N METI3 52 " --> pdb=" O ILEI3 135 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SERI3 137 " --> pdb=" O GLYI3 50 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLYI3 50 " --> pdb=" O SERI3 137 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARGI3 139 " --> pdb=" O LEUI3 48 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEUI3 48 " --> pdb=" O ARGI3 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I3' and resid 59 through 61 removed outlier: 6.830A pdb=" N ILEI3 97 " --> pdb=" O GLNI3 123 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THRI3 125 " --> pdb=" O HISI3 95 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HISI3 95 " --> pdb=" O THRI3 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I3' and resid 190 through 193 removed outlier: 3.537A pdb=" N GLYI3 196 " --> pdb=" O ASPI3 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J3' and resid 49 through 52 removed outlier: 6.338A pdb=" N VALJ3 49 " --> pdb=" O VALJ3 70 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALJ3 70 " --> pdb=" O VALJ3 49 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SERJ3 51 " --> pdb=" O ILEJ3 68 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILEJ3 17 " --> pdb=" O GLYJ3 135 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLYJ3 135 " --> pdb=" O ILEJ3 17 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J3' and resid 93 through 95 Processing sheet with id=AD7, first strand: chain 'L3' and resid 22 through 24 removed outlier: 6.231A pdb=" N ALAL3 23 " --> pdb=" O LEUN3 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'L3' and resid 58 through 60 Processing sheet with id=AD9, first strand: chain 'L3' and resid 124 through 126 Processing sheet with id=AE1, first strand: chain 'M3' and resid 45 through 51 removed outlier: 4.832A pdb=" N ARGM3 47 " --> pdb=" O VALM3 38 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VALM3 38 " --> pdb=" O ARGM3 47 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALAM3 49 " --> pdb=" O ALAM3 36 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALAM3 36 " --> pdb=" O ALAM3 49 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARGM3 35 " --> pdb=" O ILEM3 31 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASPM3 39 " --> pdb=" O ILEM3 27 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILEM3 27 " --> pdb=" O ASPM3 39 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARGM3 11 " --> pdb=" O ILEM3 27 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VALM3 12 " --> pdb=" O THRM3 58 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N3' and resid 36 through 39 removed outlier: 4.729A pdb=" N ILEN3 61 " --> pdb=" O ALAN3 39 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHEN3 129 " --> pdb=" O TRPN3 120 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRPN3 120 " --> pdb=" O PHEN3 129 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLUN3 131 " --> pdb=" O SERN3 118 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SERN3 118 " --> pdb=" O GLUN3 131 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILEN3 133 " --> pdb=" O LEUN3 116 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O3' and resid 7 through 10 removed outlier: 6.221A pdb=" N LEUO3 7 " --> pdb=" O VALO3 34 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VALO3 36 " --> pdb=" O LEUO3 7 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEUO3 9 " --> pdb=" O VALO3 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'O3' and resid 42 through 44 Processing sheet with id=AE5, first strand: chain 'P3' and resid 16 through 22 removed outlier: 6.099A pdb=" N LYSP3 16 " --> pdb=" O LEUP3 150 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEUP3 150 " --> pdb=" O LYSP3 16 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARGP3 18 " --> pdb=" O METP3 148 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N METP3 148 " --> pdb=" O ARGP3 18 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N SERP3 20 " --> pdb=" O ILEP3 146 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILEP3 146 " --> pdb=" O SERP3 20 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N HISP3 145 " --> pdb=" O VALP3 119 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VALP3 119 " --> pdb=" O HISP3 145 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLUP3 147 " --> pdb=" O ILEP3 117 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILEP3 117 " --> pdb=" O GLUP3 147 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILEP3 149 " --> pdb=" O GLUP3 115 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P3' and resid 58 through 59 Processing sheet with id=AE7, first strand: chain 'P3' and resid 128 through 130 Processing sheet with id=AE8, first strand: chain 'Q3' and resid 61 through 62 removed outlier: 6.216A pdb=" N LEUQ3 61 " --> pdb=" O THRQ3 87 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q3' and resid 120 through 121 removed outlier: 6.314A pdb=" N VALQ3 100 " --> pdb=" O LEUQ3 121 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THRQ3 79 " --> pdb=" O VALQ3 137 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R3' and resid 22 through 24 Processing sheet with id=AF2, first strand: chain 'S3' and resid 59 through 66 removed outlier: 5.209A pdb=" N ILES3 61 " --> pdb=" O ARGS3 15 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARGS3 15 " --> pdb=" O ILES3 61 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S3' and resid 95 through 99 Processing sheet with id=AF4, first strand: chain 'S3' and resid 83 through 85 Processing sheet with id=AF5, first strand: chain 'T3' and resid 83 through 89 removed outlier: 6.532A pdb=" N GLYT3 73 " --> pdb=" O TYRT3 65 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARGT3 63 " --> pdb=" O VALT3 75 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASNT3 77 " --> pdb=" O THRT3 61 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THRT3 61 " --> pdb=" O ASNT3 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U3' and resid 62 through 66 removed outlier: 3.829A pdb=" N LYSU3 69 " --> pdb=" O SERU3 66 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TYRU3 110 " --> pdb=" O LYSU3 20 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THRU3 22 " --> pdb=" O TYRU3 110 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEUU3 112 " --> pdb=" O THRU3 22 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASPU3 24 " --> pdb=" O LEUU3 112 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N TYRU3 114 " --> pdb=" O ASPU3 24 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V3' and resid 20 through 21 Processing sheet with id=AF8, first strand: chain 'V3' and resid 36 through 38 removed outlier: 8.576A pdb=" N GLYV3 103 " --> pdb=" O VALV3 25 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASNV3 27 " --> pdb=" O GLYV3 103 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ILEV3 105 " --> pdb=" O ASNV3 27 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VALV3 104 " --> pdb=" O VALV3 81 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VALV3 81 " --> pdb=" O VALV3 104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V3' and resid 88 through 90 removed outlier: 3.618A pdb=" N VALV3 94 " --> pdb=" O ARGV3 90 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHEV3 95 " --> pdb=" O ARGW3 20 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALAW3 22 " --> pdb=" O PHEV3 95 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYRV3 97 " --> pdb=" O ALAW3 22 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARGW3 23 " --> pdb=" O LYSW3 27 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LYSW3 27 " --> pdb=" O ARGW3 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W3' and resid 4 through 5 Processing sheet with id=AG2, first strand: chain 'X3' and resid 77 through 80 removed outlier: 3.645A pdb=" N PHEX3 79 " --> pdb=" O ILEX3 99 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYSX3 134 " --> pdb=" O VALX3 100 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYSX3 135 " --> pdb=" O THRX3 126 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THRX3 126 " --> pdb=" O LYSX3 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYRX3 137 " --> pdb=" O VALX3 124 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VALX3 124 " --> pdb=" O TYRX3 137 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARGX3 139 " --> pdb=" O ALAX3 122 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y3' and resid 31 through 33 Processing sheet with id=AG4, first strand: chain 'Y3' and resid 79 through 82 removed outlier: 6.738A pdb=" N VALY3 79 " --> pdb=" O VALY3 73 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VALY3 73 " --> pdb=" O VALY3 79 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYRY3 81 " --> pdb=" O VALY3 71 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLUY3 54 " --> pdb=" O THRY3 107 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y3' and resid 86 through 88 Processing sheet with id=AG6, first strand: chain 'Z3' and resid 69 through 76 removed outlier: 6.505A pdb=" N LYSZ3 69 " --> pdb=" O ASPZ3 47 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HISZ3 40 " --> pdb=" O ASNZ3 28 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASNZ3 28 " --> pdb=" O HISZ3 40 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEUZ3 42 " --> pdb=" O VALZ3 26 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALZ3 24 " --> pdb=" O ALAZ3 44 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYSZ3 22 " --> pdb=" O ILEZ3 46 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYSZ3 9 " --> pdb=" O ILEZ3 25 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VALZ3 10 " --> pdb=" O THRZ3 83 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a3' and resid 72 through 74 removed outlier: 5.735A pdb=" N VALa3 73 " --> pdb=" O LEUa3 112 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a3' and resid 100 through 102 removed outlier: 6.633A pdb=" N ILEa3 101 " --> pdb=" O LYSa3 125 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'c3' and resid 26 through 29 removed outlier: 6.342A pdb=" N LYSc3 26 " --> pdb=" O ILEc3 97 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEUc3 45 " --> pdb=" O ILEc3 96 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VALc3 46 " --> pdb=" O HISc3 72 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'd3' and resid 22 through 26 removed outlier: 6.522A pdb=" N ARGd3 63 " --> pdb=" O VALd3 106 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N TYRd3 108 " --> pdb=" O ARGd3 63 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'e3' and resid 78 through 79 Processing sheet with id=AH3, first strand: chain 'f3' and resid 62 through 71 removed outlier: 8.743A pdb=" N GLYf3 62 " --> pdb=" O THRf3 57 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N THRf3 57 " --> pdb=" O GLYf3 62 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N ASNf3 55 " --> pdb=" O PROf3 64 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LYSf3 66 " --> pdb=" O ALAf3 53 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VALf3 50 " --> pdb=" O ARGf3 100 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARGf3 100 " --> pdb=" O VALf3 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEf3 101 " --> pdb=" O ALAf3 9 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHEf3 11 " --> pdb=" O LYSf3 29 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYSf3 29 " --> pdb=" O PHEf3 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLYf3 13 " --> pdb=" O LEUf3 27 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THRf3 25 " --> pdb=" O LYSf3 15 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N METf3 83 " --> pdb=" O HISf3 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARGf3 76 " --> pdb=" O ARGf3 85 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'g3' and resid 22 through 24 Processing sheet with id=AH5, first strand: chain 'j3' and resid 16 through 17 removed outlier: 3.672A pdb=" N THRj3 33 " --> pdb=" O HISj3 28 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'k3' and resid 3 through 4 removed outlier: 6.902A pdb=" N ARGk3 3 " --> pdb=" O THRk3 44 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'k3' and resid 3 through 4 removed outlier: 6.902A pdb=" N ARGk3 3 " --> pdb=" O THRk3 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYSk3 33 " --> pdb=" O LYSk3 26 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SERk3 22 " --> pdb=" O ARGk3 37 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VALk3 23 " --> pdb=" O LYSk3 67 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEUk3 69 " --> pdb=" O VALk3 23 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILEk3 25 " --> pdb=" O LEUk3 69 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'm3' and resid 76 through 77 Processing sheet with id=AH9, first strand: chain 'o3' and resid 3 through 4 Processing sheet with id=AI1, first strand: chain 'o3' and resid 9 through 11 removed outlier: 3.531A pdb=" N ILEo3 66 " --> pdb=" O ILEo3 85 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'p3' and resid 48 through 49 Processing sheet with id=AI3, first strand: chain 'r3' and resid 17 through 20 Processing sheet with id=AI4, first strand: chain 'r3' and resid 49 through 53 Processing sheet with id=AI5, first strand: chain 's3' and resid 52 through 54 Processing sheet with id=AI6, first strand: chain 't3' and resid 11 through 13 removed outlier: 3.918A pdb=" N ILEt3 64 " --> pdb=" O LYSt3 11 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEUt3 62 " --> pdb=" O VALt3 13 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'NA' and resid 102 through 103 Processing sheet with id=AI8, first strand: chain 'NA' and resid 120 through 122 removed outlier: 4.311A pdb=" N ILENB 90 " --> pdb=" O TYRNA 120 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VALNB 79 " --> pdb=" O ILENB 56 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'NB' and resid 62 through 64 removed outlier: 3.823A pdb=" N VALNB 62 " --> pdb=" O PHENB 74 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HISNB 93 " --> pdb=" O ASNNB 75 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'TT' and resid 379 through 380 Processing sheet with id=AJ2, first strand: chain 'TT' and resid 388 through 389 Processing sheet with id=AJ3, first strand: chain 'TT' and resid 393 through 394 Processing sheet with id=AJ4, first strand: chain 'TT' and resid 417 through 418 removed outlier: 6.508A pdb=" N METTT 417 " --> pdb=" O VALTT 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 1825 hydrogen bonds defined for protein. 5001 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2652 hydrogen bonds 4464 hydrogen bond angles 0 basepair planarities 1065 basepair parallelities 2111 stacking parallelities Total time for adding SS restraints: 264.75 Time building geometry restraints manager: 60.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 16907 1.32 - 1.44: 63022 1.44 - 1.57: 65663 1.57 - 1.69: 7743 1.69 - 1.82: 427 Bond restraints: 153762 Sorted by residual: bond pdb=" CA GLNC3 61 " pdb=" C GLNC3 61 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.41e-02 5.03e+03 2.67e+01 bond pdb=" CA GLNG3 135 " pdb=" C GLNG3 135 " ideal model delta sigma weight residual 1.522 1.452 0.069 1.72e-02 3.38e+03 1.62e+01 bond pdb=" CA SERj3 50 " pdb=" CB SERj3 50 " ideal model delta sigma weight residual 1.527 1.432 0.096 2.48e-02 1.63e+03 1.49e+01 bond pdb=" N ILE 1 7 " pdb=" CA ILE 1 7 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.07e-02 8.73e+03 1.22e+01 bond pdb=" N VAL 1 5 " pdb=" CA VAL 1 5 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.92e+00 ... (remaining 153757 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.41: 19758 105.41 - 113.05: 91608 113.05 - 120.69: 67613 120.69 - 128.32: 41417 128.32 - 135.96: 6001 Bond angle restraints: 226397 Sorted by residual: angle pdb=" N ALANI 17 " pdb=" CA ALANI 17 " pdb=" C ALANI 17 " ideal model delta sigma weight residual 107.73 114.72 -6.99 1.34e+00 5.57e-01 2.72e+01 angle pdb=" O3' G543904 " pdb=" C3' G543904 " pdb=" C2' G543904 " ideal model delta sigma weight residual 109.50 116.69 -7.19 1.50e+00 4.44e-01 2.30e+01 angle pdb=" N GLYC3 98 " pdb=" CA GLYC3 98 " pdb=" C GLYC3 98 " ideal model delta sigma weight residual 113.18 102.65 10.53 2.37e+00 1.78e-01 1.97e+01 angle pdb=" CA LEUC3 150 " pdb=" CB LEUC3 150 " pdb=" CG LEUC3 150 " ideal model delta sigma weight residual 116.30 101.42 14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" N VALr3 10 " pdb=" CA VALr3 10 " pdb=" CB VALr3 10 " ideal model delta sigma weight residual 112.07 105.63 6.44 1.52e+00 4.33e-01 1.79e+01 ... (remaining 226392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 87918 35.87 - 71.73: 9941 71.73 - 107.60: 1338 107.60 - 143.46: 38 143.46 - 179.33: 79 Dihedral angle restraints: 99314 sinusoidal: 77975 harmonic: 21339 Sorted by residual: dihedral pdb=" O4' C542627 " pdb=" C1' C542627 " pdb=" N1 C542627 " pdb=" C2 C542627 " ideal model delta sinusoidal sigma weight residual -160.00 19.31 -179.31 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C544759 " pdb=" C1' C544759 " pdb=" N1 C544759 " pdb=" C2 C544759 " ideal model delta sinusoidal sigma weight residual 200.00 21.94 178.06 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U544869 " pdb=" C1' U544869 " pdb=" N1 U544869 " pdb=" C2 U544869 " ideal model delta sinusoidal sigma weight residual -160.00 17.30 -177.30 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 99311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 25823 0.082 - 0.164: 2244 0.164 - 0.245: 114 0.245 - 0.327: 19 0.327 - 0.409: 3 Chirality restraints: 28203 Sorted by residual: chirality pdb=" C3' G541329 " pdb=" C4' G541329 " pdb=" O3' G541329 " pdb=" C2' G541329 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C3' G543904 " pdb=" C4' G543904 " pdb=" O3' G543904 " pdb=" C2' G543904 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C3' A543876 " pdb=" C4' A543876 " pdb=" O3' A543876 " pdb=" C2' A543876 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 28200 not shown) Planarity restraints: 14170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G54 978 " -0.048 2.00e-02 2.50e+03 2.19e-02 1.43e+01 pdb=" N9 G54 978 " 0.055 2.00e-02 2.50e+03 pdb=" C8 G54 978 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G54 978 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G54 978 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G54 978 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G54 978 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G54 978 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G54 978 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G54 978 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G54 978 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G54 978 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PROO3 110 " 0.052 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PROO3 111 " -0.134 5.00e-02 4.00e+02 pdb=" CA PROO3 111 " 0.038 5.00e-02 4.00e+02 pdb=" CD PROO3 111 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYRN3 62 " 0.022 2.00e-02 2.50e+03 2.02e-02 8.14e+00 pdb=" CG TYRN3 62 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYRN3 62 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYRN3 62 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYRN3 62 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYRN3 62 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYRN3 62 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYRN3 62 " 0.004 2.00e-02 2.50e+03 ... (remaining 14167 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 27 1.90 - 2.65: 6773 2.65 - 3.40: 176498 3.40 - 4.15: 451220 4.15 - 4.90: 672553 Nonbonded interactions: 1307071 Sorted by model distance: nonbonded pdb="MG MG545133 " pdb="MG MG545233 " model vdw 1.148 1.300 nonbonded pdb="MG MG545218 " pdb="MG MG545220 " model vdw 1.173 1.300 nonbonded pdb=" NH1 ARGTT 196 " pdb=" OE2 GLU 1 3 " model vdw 1.256 2.520 nonbonded pdb=" O3' A23 76 " pdb=" C VAL 1 64 " model vdw 1.268 3.270 nonbonded pdb=" CD2 LEUTT 277 " pdb=" CD1 ILE 1 4 " model vdw 1.411 3.880 ... (remaining 1307066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.650 Construct map_model_manager: 0.140 Extract box with map and model: 17.700 Check model and map are aligned: 1.520 Set scattering table: 1.000 Process input model: 545.670 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.400 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 577.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0102 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 0.128 153762 Z= 0.678 Angle : 0.831 17.672 226397 Z= 0.432 Chirality : 0.048 0.409 28203 Planarity : 0.005 0.077 14170 Dihedral : 23.923 179.326 85552 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.94 % Favored : 90.96 % Rotamer: Outliers : 0.76 % Allowed : 10.86 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.08), residues: 7271 helix: -4.25 (0.06), residues: 2392 sheet: -3.08 (0.14), residues: 967 loop : -2.81 (0.08), residues: 3912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRPj3 49 HIS 0.021 0.002 HISB3 245 PHE 0.021 0.002 PHEI3 34 TYR 0.048 0.003 TYRN3 62 ARG 0.018 0.001 ARGQ3 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 670 time to evaluate : 6.572 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: D3 293 ARG cc_start: 0.5312 (ttt180) cc_final: 0.4819 (mtm-85) REVERT: H3 105 ILE cc_start: -0.0501 (OUTLIER) cc_final: -0.1271 (mt) REVERT: P3 148 MET cc_start: -0.3066 (ptp) cc_final: -0.3451 (mmt) REVERT: R3 3 MET cc_start: -0.0700 (tpt) cc_final: -0.2461 (tpp) REVERT: Z3 123 LYS cc_start: 0.5550 (mttm) cc_final: 0.4840 (mmtt) REVERT: c3 22 MET cc_start: -0.1145 (mmt) cc_final: -0.2485 (mmp) REVERT: d3 57 MET cc_start: -0.2477 (mtt) cc_final: -0.2903 (mtt) REVERT: d3 86 VAL cc_start: 0.0093 (OUTLIER) cc_final: -0.0642 (t) REVERT: i3 43 MET cc_start: 0.2585 (tpp) cc_final: 0.0631 (ttt) REVERT: i3 97 MET cc_start: -0.1111 (mtm) cc_final: -0.1530 (ppp) REVERT: k3 34 PHE cc_start: 0.1049 (m-80) cc_final: 0.0329 (m-80) REVERT: n3 10 MET cc_start: 0.2741 (mtp) cc_final: 0.1269 (tpp) REVERT: o3 82 MET cc_start: 0.1219 (mmt) cc_final: 0.0791 (mmt) REVERT: s3 12 ASN cc_start: 0.2219 (t0) cc_final: 0.1949 (t0) REVERT: s3 46 SER cc_start: 0.4182 (p) cc_final: 0.3886 (m) REVERT: s3 47 LEU cc_start: 0.4428 (mm) cc_final: 0.4079 (tp) REVERT: s3 177 MET cc_start: 0.0427 (tpp) cc_final: -0.0536 (mtt) REVERT: t3 78 SER cc_start: 0.3914 (t) cc_final: 0.3410 (p) REVERT: t3 107 ASP cc_start: 0.3703 (m-30) cc_final: 0.3303 (t70) REVERT: TT 291 GLU cc_start: 0.2007 (tp30) cc_final: 0.1767 (mt-10) REVERT: TT 310 ARG cc_start: 0.1515 (ttm110) cc_final: 0.1127 (mmt180) outliers start: 48 outliers final: 16 residues processed: 713 average time/residue: 1.4110 time to fit residues: 1679.5832 Evaluate side-chains 426 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 408 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B3 residue 90 VAL Chi-restraints excluded: chain B3 residue 207 VAL Chi-restraints excluded: chain E3 residue 178 VAL Chi-restraints excluded: chain H3 residue 105 ILE Chi-restraints excluded: chain L3 residue 154 VAL Chi-restraints excluded: chain N3 residue 80 THR Chi-restraints excluded: chain N3 residue 155 VAL Chi-restraints excluded: chain P3 residue 24 VAL Chi-restraints excluded: chain Y3 residue 79 VAL Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain j3 residue 67 LEU Chi-restraints excluded: chain j3 residue 82 THR Chi-restraints excluded: chain p3 residue 16 THR Chi-restraints excluded: chain p3 residue 52 VAL Chi-restraints excluded: chain 1 residue 3 GLU Chi-restraints excluded: chain 1 residue 6 HIS Chi-restraints excluded: chain 1 residue 49 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 931 optimal weight: 3.9990 chunk 836 optimal weight: 0.6980 chunk 463 optimal weight: 0.9980 chunk 285 optimal weight: 0.8980 chunk 563 optimal weight: 0.7980 chunk 446 optimal weight: 3.9990 chunk 864 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 525 optimal weight: 0.9980 chunk 643 optimal weight: 3.9990 chunk 1001 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 194 ASN B3 145 GLN B3 258 HIS ** B3 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 354 GLN C3 119 GLN C3 178 ASN C3 198 ASN D3 175 HIS D3 198 HIS E3 253 GLN F3 55 HIS ** F3 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G3 138 GLN G3 147 GLN G3 194 ASN G3 206 GLN I3 59 GLN I3 73 ASN I3 202 ASN ** J3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J3 97 ASN J3 104 ASN L3 15 HIS L3 67 HIS L3 113 ASN L3 115 GLN L3 188 ASN ** N3 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N3 87 HIS N3 99 GLN N3 178 HIS N3 196 ASN O3 150 GLN ** O3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O3 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 56 GLN P3 118 GLN P3 120 ASN ** Q3 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 57 ASN Q3 160 HIS R3 7 GLN R3 39 GLN R3 86 ASN R3 143 HIS S3 37 HIS S3 91 HIS S3 92 ASN S3 163 HIS T3 114 GLN T3 127 GLN U3 105 ASN X3 93 ASN X3 105 ASN X3 107 HIS Y3 20 ASN ** Z3 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 14 HIS b3 49 HIS b3 60 ASN b3 61 ASN b3 101 HIS ** d3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e3 92 ASN f3 24 HIS f3 80 ASN g3 73 HIS g3 114 GLN h3 63 GLN h3 108 GLN ** i3 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j3 76 HIS l3 4 HIS p3 56 HIS r3 70 GLN s3 42 GLN ** s3 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s3 81 HIS s3 105 ASN t3 103 ASN t3 147 HIS TT 118 GLN ** TT 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TT 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 197 GLN TT 315 GLN 1 43 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0654 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 153762 Z= 0.182 Angle : 0.666 11.769 226397 Z= 0.338 Chirality : 0.038 0.289 28203 Planarity : 0.005 0.075 14170 Dihedral : 24.655 179.915 69982 Min Nonbonded Distance : 1.074 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 1.54 % Allowed : 13.93 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.09), residues: 7271 helix: -2.32 (0.09), residues: 2425 sheet: -2.44 (0.15), residues: 964 loop : -2.02 (0.09), residues: 3882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRPTT 231 HIS 0.012 0.001 HISF3 55 PHE 0.031 0.002 PHEO3 192 TYR 0.025 0.002 TYRD3 145 ARG 0.024 0.001 ARGD3 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 467 time to evaluate : 6.675 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: C3 94 ASN cc_start: 0.0024 (OUTLIER) cc_final: -0.2318 (p0) REVERT: D3 69 ILE cc_start: 0.2947 (tt) cc_final: 0.2550 (tt) REVERT: D3 293 ARG cc_start: 0.5476 (ttt180) cc_final: 0.4724 (mtm180) REVERT: J3 22 LEU cc_start: 0.3016 (mt) cc_final: 0.2642 (mt) REVERT: M3 50 MET cc_start: 0.3265 (mpp) cc_final: 0.2445 (mtm) REVERT: O3 118 MET cc_start: 0.1332 (OUTLIER) cc_final: 0.1106 (mmp) REVERT: P3 125 MET cc_start: 0.1346 (ptm) cc_final: -0.0018 (ptp) REVERT: P3 148 MET cc_start: -0.2892 (ptp) cc_final: -0.3573 (mmp) REVERT: Q3 174 PHE cc_start: -0.0875 (m-80) cc_final: -0.1445 (m-80) REVERT: R3 3 MET cc_start: -0.0155 (tpt) cc_final: -0.1059 (tpt) REVERT: R3 89 MET cc_start: 0.0989 (mmm) cc_final: 0.0768 (mmt) REVERT: R3 139 MET cc_start: 0.1639 (ttp) cc_final: 0.0964 (ttt) REVERT: S3 54 MET cc_start: 0.2391 (OUTLIER) cc_final: 0.2017 (mmt) REVERT: T3 146 LYS cc_start: 0.3669 (tmtt) cc_final: 0.3444 (ptpp) REVERT: V3 90 ARG cc_start: 0.0978 (ptp-170) cc_final: 0.0763 (ptp-170) REVERT: W3 1 MET cc_start: 0.2663 (tpp) cc_final: 0.1822 (mmt) REVERT: Z3 123 LYS cc_start: 0.5836 (mttm) cc_final: 0.5093 (mmtt) REVERT: c3 22 MET cc_start: -0.1186 (mmt) cc_final: -0.3578 (mmt) REVERT: c3 37 MET cc_start: 0.2255 (ptt) cc_final: 0.2022 (mtm) REVERT: f3 80 ASN cc_start: 0.1729 (OUTLIER) cc_final: 0.0887 (t0) REVERT: k3 34 PHE cc_start: 0.1408 (m-80) cc_final: 0.0552 (m-80) REVERT: n3 10 MET cc_start: 0.1726 (mtp) cc_final: 0.0803 (ttm) REVERT: s3 177 MET cc_start: 0.0862 (tpp) cc_final: 0.0229 (mtt) REVERT: t3 78 SER cc_start: 0.3646 (t) cc_final: 0.3086 (p) REVERT: t3 107 ASP cc_start: 0.4187 (m-30) cc_final: 0.3797 (t70) REVERT: t3 146 ARG cc_start: 0.5550 (ptt-90) cc_final: 0.4757 (ttt180) REVERT: NA 80 MET cc_start: 0.3769 (mtm) cc_final: 0.2354 (mmp) REVERT: TT 204 ASP cc_start: 0.3175 (OUTLIER) cc_final: 0.2744 (m-30) REVERT: 1 1 MET cc_start: 0.2930 (mpp) cc_final: 0.2436 (mpp) outliers start: 97 outliers final: 41 residues processed: 543 average time/residue: 1.2770 time to fit residues: 1197.3477 Evaluate side-chains 428 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 382 time to evaluate : 6.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A3 residue 32 VAL Chi-restraints excluded: chain A3 residue 207 VAL Chi-restraints excluded: chain B3 residue 53 MET Chi-restraints excluded: chain B3 residue 56 ILE Chi-restraints excluded: chain B3 residue 57 VAL Chi-restraints excluded: chain B3 residue 207 VAL Chi-restraints excluded: chain C3 residue 94 ASN Chi-restraints excluded: chain D3 residue 75 VAL Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain E3 residue 197 VAL Chi-restraints excluded: chain E3 residue 291 PHE Chi-restraints excluded: chain I3 residue 36 LEU Chi-restraints excluded: chain J3 residue 70 VAL Chi-restraints excluded: chain L3 residue 154 VAL Chi-restraints excluded: chain M3 residue 83 ASN Chi-restraints excluded: chain N3 residue 19 MET Chi-restraints excluded: chain N3 residue 56 LYS Chi-restraints excluded: chain N3 residue 80 THR Chi-restraints excluded: chain N3 residue 178 HIS Chi-restraints excluded: chain O3 residue 118 MET Chi-restraints excluded: chain P3 residue 2 VAL Chi-restraints excluded: chain P3 residue 118 GLN Chi-restraints excluded: chain Q3 residue 42 THR Chi-restraints excluded: chain Q3 residue 79 THR Chi-restraints excluded: chain Q3 residue 105 VAL Chi-restraints excluded: chain S3 residue 54 MET Chi-restraints excluded: chain T3 residue 40 VAL Chi-restraints excluded: chain U3 residue 60 VAL Chi-restraints excluded: chain U3 residue 103 VAL Chi-restraints excluded: chain Y3 residue 79 VAL Chi-restraints excluded: chain Y3 residue 82 ILE Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain f3 residue 80 ASN Chi-restraints excluded: chain g3 residue 48 VAL Chi-restraints excluded: chain i3 residue 77 VAL Chi-restraints excluded: chain j3 residue 67 LEU Chi-restraints excluded: chain k3 residue 36 VAL Chi-restraints excluded: chain l3 residue 27 ILE Chi-restraints excluded: chain p3 residue 16 THR Chi-restraints excluded: chain p3 residue 52 VAL Chi-restraints excluded: chain s3 residue 176 ASN Chi-restraints excluded: chain t3 residue 74 VAL Chi-restraints excluded: chain TT residue 204 ASP Chi-restraints excluded: chain 1 residue 49 VAL Chi-restraints excluded: chain 1 residue 61 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 556 optimal weight: 0.7980 chunk 310 optimal weight: 0.7980 chunk 833 optimal weight: 7.9990 chunk 682 optimal weight: 20.0000 chunk 276 optimal weight: 0.6980 chunk 1003 optimal weight: 10.0000 chunk 1084 optimal weight: 7.9990 chunk 893 optimal weight: 7.9990 chunk 995 optimal weight: 9.9990 chunk 342 optimal weight: 0.9980 chunk 805 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 42 HIS B3 158 GLN ** B3 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 119 GLN ** D3 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E3 269 GLN F3 57 HIS F3 115 GLN G3 91 ASN G3 280 ASN H3 116 ASN J3 42 GLN J3 98 ASN L3 188 ASN M3 20 HIS N3 8 GLN N3 156 HIS N3 196 ASN N3 201 HIS ** O3 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O3 167 HIS P3 25 HIS P3 118 GLN ** P3 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 7 HIS ** Q3 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 57 ASN R3 75 HIS S3 50 GLN ** T3 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X3 108 GLN ** Z3 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c3 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d3 30 HIS e3 92 ASN ** j3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t3 103 ASN t3 137 GLN TT 118 GLN ** TT 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TT 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 197 GLN TT 226 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1626 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.230 153762 Z= 0.267 Angle : 0.795 18.054 226397 Z= 0.405 Chirality : 0.043 0.423 28203 Planarity : 0.007 0.140 14170 Dihedral : 24.835 179.966 69969 Min Nonbonded Distance : 0.984 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 3.21 % Allowed : 15.97 % Favored : 80.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.69 (0.09), residues: 7271 helix: -1.62 (0.09), residues: 2420 sheet: -2.05 (0.15), residues: 947 loop : -1.78 (0.09), residues: 3904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRPR3 95 HIS 0.077 0.002 HISN3 178 PHE 0.035 0.003 PHEC3 257 TYR 0.040 0.003 TYRI3 17 ARG 0.056 0.001 ARGR3 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 433 time to evaluate : 6.418 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: A3 107 MET cc_start: -0.1033 (mtt) cc_final: -0.1817 (ptp) REVERT: B3 171 LEU cc_start: -0.0719 (OUTLIER) cc_final: -0.1005 (tp) REVERT: B3 216 MET cc_start: -0.1992 (OUTLIER) cc_final: -0.3073 (tmm) REVERT: B3 351 LEU cc_start: 0.3437 (OUTLIER) cc_final: 0.2813 (tp) REVERT: C3 94 ASN cc_start: 0.0762 (OUTLIER) cc_final: -0.0712 (p0) REVERT: C3 101 MET cc_start: 0.1813 (OUTLIER) cc_final: -0.0848 (mmp) REVERT: C3 118 THR cc_start: -0.0570 (OUTLIER) cc_final: -0.0786 (t) REVERT: C3 219 LYS cc_start: 0.1025 (OUTLIER) cc_final: -0.0272 (mttm) REVERT: E3 64 MET cc_start: 0.4072 (ptt) cc_final: 0.2561 (mtp) REVERT: E3 217 ASP cc_start: 0.3540 (OUTLIER) cc_final: 0.2306 (p0) REVERT: F3 73 MET cc_start: 0.4283 (tpp) cc_final: 0.4080 (ttp) REVERT: H3 80 MET cc_start: -0.1012 (ttm) cc_final: -0.1905 (tpt) REVERT: J3 15 LEU cc_start: 0.2665 (OUTLIER) cc_final: 0.2419 (tp) REVERT: M3 50 MET cc_start: 0.4088 (OUTLIER) cc_final: 0.3359 (mtm) REVERT: N3 50 ARG cc_start: 0.1778 (mtm-85) cc_final: 0.1462 (mtt180) REVERT: N3 150 TRP cc_start: 0.2485 (OUTLIER) cc_final: 0.0470 (p-90) REVERT: O3 42 ASN cc_start: 0.2138 (OUTLIER) cc_final: 0.1413 (t0) REVERT: O3 161 LYS cc_start: 0.0747 (OUTLIER) cc_final: -0.0230 (mttt) REVERT: P3 125 MET cc_start: 0.2483 (ptm) cc_final: 0.1110 (ptp) REVERT: Q3 174 PHE cc_start: 0.0311 (m-80) cc_final: -0.0566 (m-80) REVERT: R3 41 ILE cc_start: 0.0096 (OUTLIER) cc_final: -0.0205 (mt) REVERT: R3 118 HIS cc_start: 0.1316 (OUTLIER) cc_final: 0.0915 (t-90) REVERT: R3 125 LEU cc_start: 0.1307 (OUTLIER) cc_final: 0.0864 (pp) REVERT: R3 139 MET cc_start: 0.2360 (ttp) cc_final: 0.0948 (ttt) REVERT: U3 34 MET cc_start: 0.3094 (tpp) cc_final: 0.2215 (tpp) REVERT: U3 39 PHE cc_start: 0.0918 (t80) cc_final: 0.0603 (t80) REVERT: V3 90 ARG cc_start: 0.2829 (ptp-170) cc_final: 0.2381 (ptp-170) REVERT: W3 1 MET cc_start: 0.2173 (tpp) cc_final: 0.1607 (tpt) REVERT: X3 123 LYS cc_start: 0.3125 (pttt) cc_final: 0.2665 (pttt) REVERT: Y3 39 ARG cc_start: 0.1887 (mmm-85) cc_final: 0.1298 (ttp80) REVERT: Z3 123 LYS cc_start: 0.5737 (mttm) cc_final: 0.5262 (mmtt) REVERT: a3 38 MET cc_start: 0.1036 (tpp) cc_final: 0.0062 (tpp) REVERT: d3 86 VAL cc_start: -0.0507 (OUTLIER) cc_final: -0.0939 (t) REVERT: e3 69 MET cc_start: -0.0664 (ttm) cc_final: -0.1389 (ttm) REVERT: f3 80 ASN cc_start: 0.2350 (OUTLIER) cc_final: 0.1762 (t0) REVERT: f3 106 TYR cc_start: 0.3073 (OUTLIER) cc_final: 0.2628 (p90) REVERT: h3 88 THR cc_start: 0.4152 (OUTLIER) cc_final: 0.3945 (p) REVERT: i3 80 HIS cc_start: 0.1411 (OUTLIER) cc_final: -0.0218 (t-170) REVERT: k3 69 LEU cc_start: 0.0339 (OUTLIER) cc_final: -0.0276 (mm) REVERT: n3 1 MET cc_start: 0.2874 (mpp) cc_final: 0.1519 (mmm) REVERT: n3 10 MET cc_start: 0.1806 (mtp) cc_final: 0.0643 (ttm) REVERT: r3 20 ARG cc_start: 0.1182 (OUTLIER) cc_final: -0.0150 (ptt-90) REVERT: r3 103 HIS cc_start: -0.1698 (OUTLIER) cc_final: -0.1968 (t70) REVERT: s3 40 MET cc_start: 0.5821 (tmm) cc_final: 0.5086 (tpt) REVERT: s3 177 MET cc_start: 0.1859 (tpp) cc_final: 0.0827 (mtm) REVERT: t3 78 SER cc_start: 0.3847 (t) cc_final: 0.3336 (p) REVERT: t3 80 LEU cc_start: 0.4057 (tt) cc_final: 0.3813 (tp) REVERT: t3 82 ILE cc_start: 0.3208 (mm) cc_final: 0.2997 (mm) REVERT: t3 85 LEU cc_start: 0.2130 (OUTLIER) cc_final: 0.1814 (mt) REVERT: TT 106 MET cc_start: -0.1590 (ptt) cc_final: -0.1968 (tmm) REVERT: TT 286 GLU cc_start: 0.2601 (OUTLIER) cc_final: 0.2072 (tt0) REVERT: TT 350 LEU cc_start: 0.0195 (mp) cc_final: -0.0104 (mt) REVERT: 1 1 MET cc_start: 0.2663 (mpp) cc_final: 0.1728 (ptm) outliers start: 203 outliers final: 84 residues processed: 598 average time/residue: 1.2770 time to fit residues: 1331.6268 Evaluate side-chains 457 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 347 time to evaluate : 6.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B3 residue 53 MET Chi-restraints excluded: chain B3 residue 56 ILE Chi-restraints excluded: chain B3 residue 162 VAL Chi-restraints excluded: chain B3 residue 171 LEU Chi-restraints excluded: chain B3 residue 207 VAL Chi-restraints excluded: chain B3 residue 214 ASP Chi-restraints excluded: chain B3 residue 216 MET Chi-restraints excluded: chain B3 residue 240 LEU Chi-restraints excluded: chain B3 residue 258 HIS Chi-restraints excluded: chain B3 residue 347 LEU Chi-restraints excluded: chain B3 residue 351 LEU Chi-restraints excluded: chain B3 residue 395 ASP Chi-restraints excluded: chain C3 residue 79 VAL Chi-restraints excluded: chain C3 residue 94 ASN Chi-restraints excluded: chain C3 residue 101 MET Chi-restraints excluded: chain C3 residue 115 VAL Chi-restraints excluded: chain C3 residue 118 THR Chi-restraints excluded: chain C3 residue 219 LYS Chi-restraints excluded: chain D3 residue 56 THR Chi-restraints excluded: chain D3 residue 93 THR Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain D3 residue 128 ASP Chi-restraints excluded: chain D3 residue 171 LEU Chi-restraints excluded: chain D3 residue 194 VAL Chi-restraints excluded: chain E3 residue 96 THR Chi-restraints excluded: chain E3 residue 178 VAL Chi-restraints excluded: chain E3 residue 197 VAL Chi-restraints excluded: chain E3 residue 217 ASP Chi-restraints excluded: chain G3 residue 155 TYR Chi-restraints excluded: chain G3 residue 300 VAL Chi-restraints excluded: chain I3 residue 43 VAL Chi-restraints excluded: chain J3 residue 15 LEU Chi-restraints excluded: chain J3 residue 49 VAL Chi-restraints excluded: chain J3 residue 70 VAL Chi-restraints excluded: chain J3 residue 163 MET Chi-restraints excluded: chain L3 residue 154 VAL Chi-restraints excluded: chain M3 residue 38 VAL Chi-restraints excluded: chain M3 residue 50 MET Chi-restraints excluded: chain M3 residue 83 ASN Chi-restraints excluded: chain N3 residue 19 MET Chi-restraints excluded: chain N3 residue 126 THR Chi-restraints excluded: chain N3 residue 133 ILE Chi-restraints excluded: chain N3 residue 135 ILE Chi-restraints excluded: chain N3 residue 150 TRP Chi-restraints excluded: chain O3 residue 22 ILE Chi-restraints excluded: chain O3 residue 27 VAL Chi-restraints excluded: chain O3 residue 42 ASN Chi-restraints excluded: chain O3 residue 161 LYS Chi-restraints excluded: chain P3 residue 2 VAL Chi-restraints excluded: chain P3 residue 78 TRP Chi-restraints excluded: chain P3 residue 113 VAL Chi-restraints excluded: chain Q3 residue 13 VAL Chi-restraints excluded: chain Q3 residue 70 MET Chi-restraints excluded: chain Q3 residue 122 THR Chi-restraints excluded: chain R3 residue 41 ILE Chi-restraints excluded: chain R3 residue 78 ILE Chi-restraints excluded: chain R3 residue 118 HIS Chi-restraints excluded: chain R3 residue 125 LEU Chi-restraints excluded: chain S3 residue 37 HIS Chi-restraints excluded: chain S3 residue 91 HIS Chi-restraints excluded: chain S3 residue 169 THR Chi-restraints excluded: chain T3 residue 124 THR Chi-restraints excluded: chain Y3 residue 24 HIS Chi-restraints excluded: chain Y3 residue 79 VAL Chi-restraints excluded: chain Y3 residue 82 ILE Chi-restraints excluded: chain Z3 residue 85 TYR Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain c3 residue 38 ILE Chi-restraints excluded: chain c3 residue 46 VAL Chi-restraints excluded: chain c3 residue 81 LEU Chi-restraints excluded: chain d3 residue 26 THR Chi-restraints excluded: chain d3 residue 80 VAL Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain d3 residue 100 ASN Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain f3 residue 80 ASN Chi-restraints excluded: chain f3 residue 106 TYR Chi-restraints excluded: chain g3 residue 48 VAL Chi-restraints excluded: chain g3 residue 74 VAL Chi-restraints excluded: chain h3 residue 44 LEU Chi-restraints excluded: chain h3 residue 82 ASP Chi-restraints excluded: chain h3 residue 88 THR Chi-restraints excluded: chain i3 residue 80 HIS Chi-restraints excluded: chain k3 residue 8 ILE Chi-restraints excluded: chain k3 residue 36 VAL Chi-restraints excluded: chain k3 residue 69 LEU Chi-restraints excluded: chain o3 residue 24 THR Chi-restraints excluded: chain p3 residue 16 THR Chi-restraints excluded: chain p3 residue 52 VAL Chi-restraints excluded: chain p3 residue 73 THR Chi-restraints excluded: chain r3 residue 20 ARG Chi-restraints excluded: chain r3 residue 44 ILE Chi-restraints excluded: chain r3 residue 103 HIS Chi-restraints excluded: chain r3 residue 115 SER Chi-restraints excluded: chain s3 residue 46 SER Chi-restraints excluded: chain s3 residue 176 ASN Chi-restraints excluded: chain s3 residue 178 LEU Chi-restraints excluded: chain t3 residue 12 VAL Chi-restraints excluded: chain t3 residue 64 ILE Chi-restraints excluded: chain t3 residue 74 VAL Chi-restraints excluded: chain t3 residue 85 LEU Chi-restraints excluded: chain t3 residue 116 MET Chi-restraints excluded: chain TT residue 168 VAL Chi-restraints excluded: chain TT residue 277 LEU Chi-restraints excluded: chain TT residue 286 GLU Chi-restraints excluded: chain TT residue 386 ILE Chi-restraints excluded: chain TT residue 396 THR Chi-restraints excluded: chain TT residue 422 VAL Chi-restraints excluded: chain TT residue 435 ILE Chi-restraints excluded: chain 1 residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 991 optimal weight: 6.9990 chunk 754 optimal weight: 5.9990 chunk 520 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 478 optimal weight: 5.9990 chunk 673 optimal weight: 4.9990 chunk 1007 optimal weight: 7.9990 chunk 1066 optimal weight: 4.9990 chunk 526 optimal weight: 0.9990 chunk 954 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 132 ASN ** A3 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 205 ASN B3 55 HIS B3 158 GLN B3 167 GLN ** B3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 289 GLN B3 315 ASN C3 43 ASN C3 48 ASN ** C3 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 278 ASN ** D3 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 45 HIS E3 131 HIS E3 170 GLN E3 287 HIS F3 55 HIS ** F3 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 171 ASN ** F3 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3 156 ASN H3 163 GLN ** I3 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 202 ASN M3 70 GLN ** N3 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N3 199 GLN O3 26 GLN ** O3 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O3 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O3 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 28 ASN ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 8 ASN ** Q3 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 162 HIS R3 86 ASN R3 118 HIS ** R3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 122 HIS ** S3 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 156 HIS ** T3 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3 79 GLN ** T3 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U3 27 HIS ** V3 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W3 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y3 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z3 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 49 HIS a3 89 ASN b3 10 HIS ** b3 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN ** c3 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c3 50 ASN c3 77 ASN ** d3 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e3 68 HIS ** e3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h3 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m3 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m3 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o3 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o3 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r3 70 GLN ** s3 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s3 71 ASN ** s3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t3 111 ASN ** NB 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 92 GLN TT 118 GLN ** TT 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TT 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3755 moved from start: 1.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.281 153762 Z= 0.643 Angle : 1.765 28.844 226397 Z= 0.861 Chirality : 0.081 0.693 28203 Planarity : 0.015 0.408 14170 Dihedral : 26.979 179.511 69966 Min Nonbonded Distance : 0.685 Molprobity Statistics. All-atom Clashscore : 51.27 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.82 % Favored : 88.57 % Rotamer: Outliers : 7.22 % Allowed : 19.23 % Favored : 73.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.76 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.08), residues: 7271 helix: -2.82 (0.09), residues: 2258 sheet: -2.68 (0.16), residues: 792 loop : -2.74 (0.08), residues: 4221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.007 TRPTT 231 HIS 0.030 0.005 HIST3 95 PHE 0.071 0.007 PHEZ3 118 TYR 0.075 0.006 TYRr3 102 ARG 0.049 0.003 ARGa3 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 456 poor density : 743 time to evaluate : 6.415 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: A3 101 VAL cc_start: 0.3771 (OUTLIER) cc_final: 0.3325 (p) REVERT: A3 202 VAL cc_start: 0.1119 (OUTLIER) cc_final: 0.0806 (t) REVERT: A3 227 ARG cc_start: -0.1374 (OUTLIER) cc_final: -0.3253 (ttm-80) REVERT: B3 53 MET cc_start: 0.2875 (OUTLIER) cc_final: 0.2495 (tpp) REVERT: B3 275 HIS cc_start: 0.4739 (OUTLIER) cc_final: 0.4133 (m90) REVERT: C3 101 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4918 (mmt) REVERT: C3 138 MET cc_start: -0.1230 (tpt) cc_final: -0.1615 (ptp) REVERT: C3 196 MET cc_start: 0.1915 (OUTLIER) cc_final: 0.0905 (mmm) REVERT: C3 219 LYS cc_start: 0.2326 (OUTLIER) cc_final: 0.1556 (mtpt) REVERT: C3 275 SER cc_start: 0.6587 (OUTLIER) cc_final: 0.6147 (m) REVERT: C3 294 LYS cc_start: 0.5293 (ptpt) cc_final: 0.5068 (pttp) REVERT: D3 113 PHE cc_start: 0.4815 (OUTLIER) cc_final: 0.3967 (m-80) REVERT: D3 208 MET cc_start: 0.6291 (tmm) cc_final: 0.3870 (ptt) REVERT: D3 212 MET cc_start: 0.5729 (tmm) cc_final: 0.5084 (ttt) REVERT: D3 232 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.6988 (p) REVERT: D3 255 LYS cc_start: 0.6620 (mtpt) cc_final: 0.6407 (tptp) REVERT: E3 198 ILE cc_start: 0.0861 (OUTLIER) cc_final: 0.0396 (mt) REVERT: E3 265 LYS cc_start: 0.6800 (mttt) cc_final: 0.5424 (tptt) REVERT: F3 59 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6099 (mt-10) REVERT: F3 124 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6006 (mt) REVERT: I3 9 TYR cc_start: 0.2949 (m-80) cc_final: 0.1704 (m-80) REVERT: I3 52 MET cc_start: 0.6119 (ptt) cc_final: 0.5795 (ttp) REVERT: I3 184 MET cc_start: 0.3776 (mmm) cc_final: 0.3433 (mmm) REVERT: I3 191 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7442 (mm) REVERT: I3 208 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7986 (tppt) REVERT: J3 157 ILE cc_start: 0.4465 (OUTLIER) cc_final: 0.2976 (mt) REVERT: J3 174 ILE cc_start: 0.6641 (mm) cc_final: 0.6249 (mm) REVERT: L3 9 ILE cc_start: 0.3764 (OUTLIER) cc_final: 0.3495 (mm) REVERT: M3 56 GLN cc_start: 0.6038 (mt0) cc_final: 0.5585 (mt0) REVERT: M3 82 ILE cc_start: -0.0554 (OUTLIER) cc_final: -0.1278 (mm) REVERT: N3 96 ARG cc_start: 0.2096 (OUTLIER) cc_final: 0.1517 (mmm-85) REVERT: O3 105 PHE cc_start: -0.0224 (m-80) cc_final: -0.1017 (m-10) REVERT: O3 161 LYS cc_start: 0.1920 (OUTLIER) cc_final: 0.0779 (mttt) REVERT: P3 40 HIS cc_start: 0.2901 (OUTLIER) cc_final: 0.2530 (m90) REVERT: Q3 91 ARG cc_start: 0.4521 (OUTLIER) cc_final: 0.1463 (tmm-80) REVERT: R3 31 GLU cc_start: 0.3135 (OUTLIER) cc_final: 0.0115 (tt0) REVERT: R3 41 ILE cc_start: 0.0109 (OUTLIER) cc_final: -0.0478 (tt) REVERT: R3 46 LYS cc_start: 0.1457 (OUTLIER) cc_final: 0.1134 (pttt) REVERT: R3 96 MET cc_start: 0.2163 (tpp) cc_final: 0.1855 (tpp) REVERT: R3 99 MET cc_start: 0.5303 (ppp) cc_final: 0.5043 (ppp) REVERT: R3 139 MET cc_start: 0.3275 (ttp) cc_final: 0.2920 (ttt) REVERT: S3 1 MET cc_start: 0.5124 (OUTLIER) cc_final: 0.4447 (ptm) REVERT: S3 54 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.6759 (mmt) REVERT: S3 81 TRP cc_start: 0.6142 (m-90) cc_final: 0.4362 (m-90) REVERT: S3 86 SER cc_start: 0.5994 (p) cc_final: 0.5468 (t) REVERT: S3 96 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5164 (mt-10) REVERT: T3 30 TYR cc_start: 0.8037 (m-80) cc_final: 0.7687 (m-80) REVERT: T3 144 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6866 (p0) REVERT: T3 157 GLU cc_start: 0.4622 (OUTLIER) cc_final: 0.4330 (mm-30) REVERT: V3 46 LYS cc_start: 0.0251 (OUTLIER) cc_final: -0.0021 (tmtt) REVERT: V3 107 ASN cc_start: 0.5610 (OUTLIER) cc_final: 0.5210 (p0) REVERT: V3 124 GLU cc_start: 0.1137 (OUTLIER) cc_final: -0.2705 (pt0) REVERT: W3 1 MET cc_start: 0.1903 (tpp) cc_final: 0.1692 (mmm) REVERT: Y3 89 LYS cc_start: 0.5976 (mmtp) cc_final: 0.4866 (tmtt) REVERT: Z3 12 LEU cc_start: -0.2082 (OUTLIER) cc_final: -0.3126 (tt) REVERT: Z3 131 PHE cc_start: 0.2585 (m-80) cc_final: 0.1218 (m-80) REVERT: a3 64 LYS cc_start: -0.0203 (OUTLIER) cc_final: -0.0424 (ptpt) REVERT: a3 69 PHE cc_start: 0.2875 (OUTLIER) cc_final: 0.1892 (t80) REVERT: d3 77 ILE cc_start: 0.1776 (OUTLIER) cc_final: 0.1348 (tt) REVERT: e3 48 ARG cc_start: 0.0385 (OUTLIER) cc_final: -0.0031 (ptt-90) REVERT: e3 69 MET cc_start: 0.1938 (ttm) cc_final: 0.1669 (ttm) REVERT: e3 90 MET cc_start: 0.5642 (tmm) cc_final: 0.5232 (tpt) REVERT: f3 36 ARG cc_start: 0.1979 (OUTLIER) cc_final: 0.0686 (ptp-170) REVERT: f3 106 TYR cc_start: 0.4711 (OUTLIER) cc_final: 0.3900 (p90) REVERT: g3 89 ASP cc_start: 0.2660 (m-30) cc_final: 0.2200 (m-30) REVERT: i3 26 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.5477 (t-90) REVERT: i3 43 MET cc_start: 0.3121 (tpt) cc_final: 0.1151 (ttt) REVERT: i3 89 GLU cc_start: 0.4195 (OUTLIER) cc_final: 0.3610 (pp20) REVERT: j3 79 ARG cc_start: 0.3497 (OUTLIER) cc_final: 0.2854 (ttp-110) REVERT: l3 25 GLN cc_start: 0.3436 (OUTLIER) cc_final: 0.2706 (mm-40) REVERT: p3 61 MET cc_start: -0.0319 (mtp) cc_final: -0.0584 (mtp) REVERT: r3 35 ARG cc_start: 0.3847 (OUTLIER) cc_final: 0.2088 (ptt180) REVERT: t3 46 ILE cc_start: 0.2227 (OUTLIER) cc_final: 0.2023 (tt) REVERT: t3 87 GLU cc_start: 0.2774 (OUTLIER) cc_final: 0.2422 (mm-30) REVERT: NB 63 ASN cc_start: 0.2149 (OUTLIER) cc_final: 0.1798 (m110) REVERT: TT 174 CYS cc_start: 0.1580 (OUTLIER) cc_final: 0.1154 (m) REVERT: TT 205 GLU cc_start: 0.4683 (mm-30) cc_final: 0.4431 (mt-10) REVERT: TT 286 GLU cc_start: 0.2253 (OUTLIER) cc_final: 0.1635 (tt0) REVERT: TT 322 ARG cc_start: 0.4029 (mmp-170) cc_final: 0.3793 (mmm160) REVERT: TT 373 LEU cc_start: 0.2297 (OUTLIER) cc_final: 0.1945 (mm) outliers start: 456 outliers final: 185 residues processed: 1102 average time/residue: 1.3740 time to fit residues: 2555.8779 Evaluate side-chains 803 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 567 time to evaluate : 6.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A3 residue 5 ILE Chi-restraints excluded: chain A3 residue 20 VAL Chi-restraints excluded: chain A3 residue 97 ASN Chi-restraints excluded: chain A3 residue 98 ILE Chi-restraints excluded: chain A3 residue 101 VAL Chi-restraints excluded: chain A3 residue 180 LEU Chi-restraints excluded: chain A3 residue 202 VAL Chi-restraints excluded: chain A3 residue 227 ARG Chi-restraints excluded: chain B3 residue 21 ARG Chi-restraints excluded: chain B3 residue 53 MET Chi-restraints excluded: chain B3 residue 90 VAL Chi-restraints excluded: chain B3 residue 153 MET Chi-restraints excluded: chain B3 residue 168 MET Chi-restraints excluded: chain B3 residue 171 LEU Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 207 VAL Chi-restraints excluded: chain B3 residue 240 LEU Chi-restraints excluded: chain B3 residue 262 VAL Chi-restraints excluded: chain B3 residue 275 HIS Chi-restraints excluded: chain B3 residue 287 ILE Chi-restraints excluded: chain B3 residue 317 LEU Chi-restraints excluded: chain B3 residue 331 VAL Chi-restraints excluded: chain B3 residue 347 LEU Chi-restraints excluded: chain B3 residue 378 ARG Chi-restraints excluded: chain B3 residue 389 MET Chi-restraints excluded: chain C3 residue 8 ILE Chi-restraints excluded: chain C3 residue 38 ASN Chi-restraints excluded: chain C3 residue 69 THR Chi-restraints excluded: chain C3 residue 89 GLN Chi-restraints excluded: chain C3 residue 101 MET Chi-restraints excluded: chain C3 residue 105 THR Chi-restraints excluded: chain C3 residue 174 LEU Chi-restraints excluded: chain C3 residue 182 LYS Chi-restraints excluded: chain C3 residue 196 MET Chi-restraints excluded: chain C3 residue 219 LYS Chi-restraints excluded: chain C3 residue 275 SER Chi-restraints excluded: chain C3 residue 279 LEU Chi-restraints excluded: chain C3 residue 292 ILE Chi-restraints excluded: chain D3 residue 9 ASN Chi-restraints excluded: chain D3 residue 75 VAL Chi-restraints excluded: chain D3 residue 81 HIS Chi-restraints excluded: chain D3 residue 113 PHE Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain D3 residue 216 GLU Chi-restraints excluded: chain D3 residue 232 THR Chi-restraints excluded: chain E3 residue 99 VAL Chi-restraints excluded: chain E3 residue 140 VAL Chi-restraints excluded: chain E3 residue 175 LEU Chi-restraints excluded: chain E3 residue 198 ILE Chi-restraints excluded: chain E3 residue 287 HIS Chi-restraints excluded: chain F3 residue 59 GLU Chi-restraints excluded: chain F3 residue 100 VAL Chi-restraints excluded: chain F3 residue 122 VAL Chi-restraints excluded: chain F3 residue 124 LEU Chi-restraints excluded: chain F3 residue 132 LEU Chi-restraints excluded: chain F3 residue 219 MET Chi-restraints excluded: chain G3 residue 155 TYR Chi-restraints excluded: chain G3 residue 198 THR Chi-restraints excluded: chain G3 residue 313 GLU Chi-restraints excluded: chain G3 residue 316 THR Chi-restraints excluded: chain H3 residue 89 ARG Chi-restraints excluded: chain H3 residue 186 THR Chi-restraints excluded: chain I3 residue 31 ILE Chi-restraints excluded: chain I3 residue 85 PHE Chi-restraints excluded: chain I3 residue 129 VAL Chi-restraints excluded: chain I3 residue 168 SER Chi-restraints excluded: chain I3 residue 191 ILE Chi-restraints excluded: chain I3 residue 212 LEU Chi-restraints excluded: chain J3 residue 26 VAL Chi-restraints excluded: chain J3 residue 34 THR Chi-restraints excluded: chain J3 residue 49 VAL Chi-restraints excluded: chain J3 residue 57 VAL Chi-restraints excluded: chain J3 residue 70 VAL Chi-restraints excluded: chain J3 residue 74 VAL Chi-restraints excluded: chain J3 residue 80 GLU Chi-restraints excluded: chain J3 residue 157 ILE Chi-restraints excluded: chain J3 residue 163 MET Chi-restraints excluded: chain L3 residue 8 MET Chi-restraints excluded: chain L3 residue 9 ILE Chi-restraints excluded: chain L3 residue 14 PHE Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 64 VAL Chi-restraints excluded: chain L3 residue 67 HIS Chi-restraints excluded: chain M3 residue 7 VAL Chi-restraints excluded: chain M3 residue 38 VAL Chi-restraints excluded: chain M3 residue 69 ARG Chi-restraints excluded: chain M3 residue 82 ILE Chi-restraints excluded: chain M3 residue 83 ASN Chi-restraints excluded: chain N3 residue 27 CYS Chi-restraints excluded: chain N3 residue 96 ARG Chi-restraints excluded: chain N3 residue 125 SER Chi-restraints excluded: chain N3 residue 126 THR Chi-restraints excluded: chain N3 residue 151 ILE Chi-restraints excluded: chain N3 residue 174 LEU Chi-restraints excluded: chain N3 residue 178 HIS Chi-restraints excluded: chain O3 residue 42 ASN Chi-restraints excluded: chain O3 residue 118 MET Chi-restraints excluded: chain O3 residue 126 VAL Chi-restraints excluded: chain O3 residue 127 VAL Chi-restraints excluded: chain O3 residue 161 LYS Chi-restraints excluded: chain O3 residue 194 ASP Chi-restraints excluded: chain P3 residue 2 VAL Chi-restraints excluded: chain P3 residue 40 HIS Chi-restraints excluded: chain P3 residue 99 GLU Chi-restraints excluded: chain P3 residue 113 VAL Chi-restraints excluded: chain P3 residue 114 ILE Chi-restraints excluded: chain P3 residue 115 GLU Chi-restraints excluded: chain P3 residue 145 HIS Chi-restraints excluded: chain Q3 residue 91 ARG Chi-restraints excluded: chain Q3 residue 129 ASP Chi-restraints excluded: chain Q3 residue 158 THR Chi-restraints excluded: chain Q3 residue 183 SER Chi-restraints excluded: chain R3 residue 31 GLU Chi-restraints excluded: chain R3 residue 41 ILE Chi-restraints excluded: chain R3 residue 45 ILE Chi-restraints excluded: chain R3 residue 46 LYS Chi-restraints excluded: chain R3 residue 55 VAL Chi-restraints excluded: chain R3 residue 78 ILE Chi-restraints excluded: chain R3 residue 95 TRP Chi-restraints excluded: chain R3 residue 121 HIS Chi-restraints excluded: chain R3 residue 125 LEU Chi-restraints excluded: chain S3 residue 1 MET Chi-restraints excluded: chain S3 residue 54 MET Chi-restraints excluded: chain S3 residue 69 GLU Chi-restraints excluded: chain S3 residue 85 ASP Chi-restraints excluded: chain S3 residue 90 THR Chi-restraints excluded: chain S3 residue 91 HIS Chi-restraints excluded: chain S3 residue 96 GLU Chi-restraints excluded: chain S3 residue 150 ILE Chi-restraints excluded: chain S3 residue 152 PHE Chi-restraints excluded: chain S3 residue 169 THR Chi-restraints excluded: chain T3 residue 25 VAL Chi-restraints excluded: chain T3 residue 40 VAL Chi-restraints excluded: chain T3 residue 96 ILE Chi-restraints excluded: chain T3 residue 109 VAL Chi-restraints excluded: chain T3 residue 124 THR Chi-restraints excluded: chain T3 residue 144 ASN Chi-restraints excluded: chain T3 residue 157 GLU Chi-restraints excluded: chain U3 residue 103 VAL Chi-restraints excluded: chain V3 residue 46 LYS Chi-restraints excluded: chain V3 residue 60 MET Chi-restraints excluded: chain V3 residue 65 VAL Chi-restraints excluded: chain V3 residue 107 ASN Chi-restraints excluded: chain V3 residue 124 GLU Chi-restraints excluded: chain X3 residue 52 LEU Chi-restraints excluded: chain X3 residue 127 LEU Chi-restraints excluded: chain Y3 residue 2 LYS Chi-restraints excluded: chain Y3 residue 7 VAL Chi-restraints excluded: chain Y3 residue 49 ILE Chi-restraints excluded: chain Y3 residue 79 VAL Chi-restraints excluded: chain Y3 residue 82 ILE Chi-restraints excluded: chain Y3 residue 88 GLU Chi-restraints excluded: chain Y3 residue 95 VAL Chi-restraints excluded: chain Z3 residue 12 LEU Chi-restraints excluded: chain Z3 residue 54 THR Chi-restraints excluded: chain Z3 residue 68 ILE Chi-restraints excluded: chain Z3 residue 85 TYR Chi-restraints excluded: chain a3 residue 12 ARG Chi-restraints excluded: chain a3 residue 14 HIS Chi-restraints excluded: chain a3 residue 43 ILE Chi-restraints excluded: chain a3 residue 58 MET Chi-restraints excluded: chain a3 residue 64 LYS Chi-restraints excluded: chain a3 residue 69 PHE Chi-restraints excluded: chain a3 residue 89 ASN Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain c3 residue 79 ILE Chi-restraints excluded: chain d3 residue 29 ILE Chi-restraints excluded: chain d3 residue 77 ILE Chi-restraints excluded: chain d3 residue 80 VAL Chi-restraints excluded: chain d3 residue 83 ARG Chi-restraints excluded: chain d3 residue 85 ARG Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain d3 residue 100 ASN Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain d3 residue 122 VAL Chi-restraints excluded: chain e3 residue 27 ARG Chi-restraints excluded: chain e3 residue 41 ILE Chi-restraints excluded: chain e3 residue 48 ARG Chi-restraints excluded: chain e3 residue 66 THR Chi-restraints excluded: chain e3 residue 91 CYS Chi-restraints excluded: chain f3 residue 36 ARG Chi-restraints excluded: chain f3 residue 106 TYR Chi-restraints excluded: chain g3 residue 32 TYR Chi-restraints excluded: chain g3 residue 48 VAL Chi-restraints excluded: chain g3 residue 82 MET Chi-restraints excluded: chain h3 residue 44 LEU Chi-restraints excluded: chain h3 residue 82 ASP Chi-restraints excluded: chain h3 residue 88 THR Chi-restraints excluded: chain i3 residue 12 ASN Chi-restraints excluded: chain i3 residue 19 LYS Chi-restraints excluded: chain i3 residue 26 HIS Chi-restraints excluded: chain i3 residue 53 TYR Chi-restraints excluded: chain i3 residue 89 GLU Chi-restraints excluded: chain j3 residue 79 ARG Chi-restraints excluded: chain j3 residue 82 THR Chi-restraints excluded: chain k3 residue 28 ASN Chi-restraints excluded: chain k3 residue 36 VAL Chi-restraints excluded: chain l3 residue 25 GLN Chi-restraints excluded: chain l3 residue 37 TYR Chi-restraints excluded: chain m3 residue 92 THR Chi-restraints excluded: chain o3 residue 5 PRO Chi-restraints excluded: chain o3 residue 63 THR Chi-restraints excluded: chain o3 residue 90 HIS Chi-restraints excluded: chain p3 residue 16 THR Chi-restraints excluded: chain p3 residue 22 LEU Chi-restraints excluded: chain p3 residue 73 THR Chi-restraints excluded: chain p3 residue 78 THR Chi-restraints excluded: chain r3 residue 10 VAL Chi-restraints excluded: chain r3 residue 20 ARG Chi-restraints excluded: chain r3 residue 35 ARG Chi-restraints excluded: chain r3 residue 37 SER Chi-restraints excluded: chain r3 residue 94 ARG Chi-restraints excluded: chain s3 residue 35 VAL Chi-restraints excluded: chain s3 residue 46 SER Chi-restraints excluded: chain s3 residue 176 ASN Chi-restraints excluded: chain t3 residue 12 VAL Chi-restraints excluded: chain t3 residue 46 ILE Chi-restraints excluded: chain t3 residue 64 ILE Chi-restraints excluded: chain t3 residue 87 GLU Chi-restraints excluded: chain t3 residue 116 MET Chi-restraints excluded: chain NB residue 63 ASN Chi-restraints excluded: chain NB residue 71 VAL Chi-restraints excluded: chain TT residue 168 VAL Chi-restraints excluded: chain TT residue 174 CYS Chi-restraints excluded: chain TT residue 184 ASN Chi-restraints excluded: chain TT residue 204 ASP Chi-restraints excluded: chain TT residue 245 THR Chi-restraints excluded: chain TT residue 277 LEU Chi-restraints excluded: chain TT residue 286 GLU Chi-restraints excluded: chain TT residue 293 LEU Chi-restraints excluded: chain TT residue 342 LEU Chi-restraints excluded: chain TT residue 358 TYR Chi-restraints excluded: chain TT residue 373 LEU Chi-restraints excluded: chain TT residue 386 ILE Chi-restraints excluded: chain TT residue 422 VAL Chi-restraints excluded: chain 1 residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 887 optimal weight: 2.9990 chunk 605 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 793 optimal weight: 4.9990 chunk 439 optimal weight: 0.6980 chunk 909 optimal weight: 2.9990 chunk 736 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 544 optimal weight: 3.9990 chunk 956 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 302 ASN B3 315 ASN B3 376 HIS C3 38 ASN ** C3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 321 ASN D3 63 GLN D3 122 GLN D3 198 HIS ** D3 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 170 GLN ** E3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 98 ASN ** G3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3 15 ASN H3 156 ASN ** I3 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 130 HIS I3 147 HIS I3 163 GLN I3 202 ASN J3 167 GLN ** J3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 87 HIS ** N3 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N3 182 HIS ** O3 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O3 90 HIS ** O3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O3 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 34 GLN ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 137 ASN Q3 44 ASN Q3 125 GLN Q3 151 HIS S3 37 HIS S3 117 HIS ** T3 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3 131 GLN V3 108 ASN W3 30 GLN ** Y3 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 89 ASN c3 77 ASN ** e3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f3 99 HIS g3 14 ASN i3 26 HIS ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o3 18 HIS ** r3 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s3 68 HIS ** s3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TT 92 GLN TT 96 GLN ** TT 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 172 HIS TT 349 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3615 moved from start: 1.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 153762 Z= 0.251 Angle : 0.851 17.135 226397 Z= 0.428 Chirality : 0.045 0.381 28203 Planarity : 0.007 0.116 14170 Dihedral : 25.856 178.919 69964 Min Nonbonded Distance : 0.914 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.07 % Favored : 93.87 % Rotamer: Outliers : 4.23 % Allowed : 22.29 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.09), residues: 7271 helix: -1.76 (0.10), residues: 2365 sheet: -2.41 (0.16), residues: 870 loop : -2.29 (0.09), residues: 4036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRPC3 267 HIS 0.030 0.002 HISE3 287 PHE 0.043 0.003 PHEa3 45 TYR 0.042 0.003 TYRB3 291 ARG 0.013 0.001 ARGP3 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 652 time to evaluate : 6.634 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: B3 389 MET cc_start: 0.4027 (mmm) cc_final: 0.3213 (ptp) REVERT: C3 86 ARG cc_start: 0.2365 (OUTLIER) cc_final: 0.1107 (tpt90) REVERT: C3 266 THR cc_start: 0.6787 (t) cc_final: 0.6544 (p) REVERT: C3 284 MET cc_start: 0.1251 (mmp) cc_final: -0.1181 (ttt) REVERT: D3 113 PHE cc_start: 0.5511 (OUTLIER) cc_final: 0.5014 (m-10) REVERT: D3 147 ASP cc_start: 0.6797 (t0) cc_final: 0.6576 (t0) REVERT: D3 208 MET cc_start: 0.6971 (tmm) cc_final: 0.6435 (ttp) REVERT: D3 236 MET cc_start: 0.8532 (mmm) cc_final: 0.8211 (mmm) REVERT: E3 118 TYR cc_start: 0.2720 (t80) cc_final: 0.2216 (t80) REVERT: F3 124 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6583 (mt) REVERT: F3 188 ASP cc_start: 0.7256 (t0) cc_final: 0.6996 (t0) REVERT: F3 235 ARG cc_start: 0.5326 (OUTLIER) cc_final: 0.5117 (ptp-170) REVERT: G3 217 ILE cc_start: 0.0309 (OUTLIER) cc_final: -0.0097 (mp) REVERT: H3 120 GLU cc_start: 0.2735 (pt0) cc_final: 0.1329 (mm-30) REVERT: I3 99 ILE cc_start: 0.6763 (tp) cc_final: 0.6525 (tp) REVERT: I3 115 MET cc_start: 0.2551 (mtp) cc_final: 0.1135 (ttt) REVERT: I3 128 ARG cc_start: 0.5935 (mtp-110) cc_final: 0.5725 (mtp85) REVERT: I3 208 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8192 (tppt) REVERT: I3 213 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.7104 (t70) REVERT: J3 12 MET cc_start: 0.8393 (mmm) cc_final: 0.8074 (mmm) REVERT: J3 81 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6249 (mm-30) REVERT: J3 174 ILE cc_start: 0.6911 (mm) cc_final: 0.6639 (mm) REVERT: L3 194 ILE cc_start: 0.3152 (tp) cc_final: 0.2859 (tp) REVERT: M3 50 MET cc_start: 0.6477 (mpp) cc_final: 0.5566 (ptp) REVERT: M3 104 MET cc_start: 0.2864 (mmp) cc_final: 0.2118 (tmm) REVERT: N3 135 ILE cc_start: 0.2887 (OUTLIER) cc_final: 0.2632 (mt) REVERT: Q3 81 VAL cc_start: 0.5494 (OUTLIER) cc_final: 0.5161 (t) REVERT: R3 31 GLU cc_start: 0.2731 (OUTLIER) cc_final: 0.0529 (tt0) REVERT: R3 41 ILE cc_start: -0.0014 (OUTLIER) cc_final: -0.0562 (tt) REVERT: R3 46 LYS cc_start: -0.0027 (OUTLIER) cc_final: -0.0479 (pttt) REVERT: R3 139 MET cc_start: 0.2793 (ttp) cc_final: 0.1634 (ttt) REVERT: S3 1 MET cc_start: 0.5050 (mmm) cc_final: 0.3568 (ttt) REVERT: S3 36 ASN cc_start: 0.8279 (p0) cc_final: 0.7944 (p0) REVERT: S3 54 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6551 (mtt) REVERT: T3 106 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.7011 (pp) REVERT: Z3 57 MET cc_start: 0.2983 (ttt) cc_final: 0.2672 (ttt) REVERT: b3 14 ARG cc_start: 0.7476 (ttp-110) cc_final: 0.6827 (mtt90) REVERT: d3 57 MET cc_start: 0.0698 (mmt) cc_final: -0.0661 (tpp) REVERT: e3 90 MET cc_start: 0.3985 (tmm) cc_final: 0.3175 (tpt) REVERT: i3 43 MET cc_start: 0.2338 (tpt) cc_final: 0.1243 (tpt) REVERT: j3 39 TYR cc_start: 0.3991 (t80) cc_final: 0.3320 (t80) REVERT: o3 82 MET cc_start: 0.8186 (mmt) cc_final: 0.7954 (mmt) REVERT: p3 4 ARG cc_start: 0.2210 (OUTLIER) cc_final: 0.1575 (mpp80) REVERT: p3 61 MET cc_start: -0.0032 (mtp) cc_final: -0.0249 (mtp) REVERT: s3 85 ASN cc_start: 0.1548 (t0) cc_final: 0.1334 (m-40) REVERT: t3 68 GLN cc_start: 0.2238 (OUTLIER) cc_final: 0.1288 (mp10) REVERT: t3 103 ASN cc_start: 0.3968 (OUTLIER) cc_final: 0.3689 (m-40) REVERT: NA 80 MET cc_start: 0.3573 (mtm) cc_final: 0.3366 (mtt) REVERT: TT 106 MET cc_start: -0.1268 (ptt) cc_final: -0.1809 (tmm) REVERT: TT 143 LYS cc_start: 0.3096 (mmmm) cc_final: 0.2622 (ttpt) REVERT: TT 205 GLU cc_start: 0.5145 (mm-30) cc_final: 0.4765 (mt-10) REVERT: TT 371 LYS cc_start: 0.2746 (ttpt) cc_final: 0.0423 (tptp) outliers start: 267 outliers final: 125 residues processed: 863 average time/residue: 1.3259 time to fit residues: 1956.9990 Evaluate side-chains 693 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 552 time to evaluate : 6.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A3 residue 6 ARG Chi-restraints excluded: chain A3 residue 47 ASP Chi-restraints excluded: chain A3 residue 112 ILE Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 165 VAL Chi-restraints excluded: chain A3 residue 204 MET Chi-restraints excluded: chain B3 residue 21 ARG Chi-restraints excluded: chain B3 residue 89 ILE Chi-restraints excluded: chain B3 residue 113 GLU Chi-restraints excluded: chain B3 residue 207 VAL Chi-restraints excluded: chain B3 residue 217 ILE Chi-restraints excluded: chain B3 residue 287 ILE Chi-restraints excluded: chain B3 residue 331 VAL Chi-restraints excluded: chain B3 residue 381 THR Chi-restraints excluded: chain C3 residue 76 ILE Chi-restraints excluded: chain C3 residue 86 ARG Chi-restraints excluded: chain C3 residue 94 ASN Chi-restraints excluded: chain C3 residue 147 VAL Chi-restraints excluded: chain C3 residue 182 LYS Chi-restraints excluded: chain C3 residue 233 THR Chi-restraints excluded: chain D3 residue 53 VAL Chi-restraints excluded: chain D3 residue 113 PHE Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain D3 residue 128 ASP Chi-restraints excluded: chain D3 residue 234 ASP Chi-restraints excluded: chain D3 residue 242 LYS Chi-restraints excluded: chain E3 residue 96 THR Chi-restraints excluded: chain E3 residue 155 ILE Chi-restraints excluded: chain E3 residue 160 HIS Chi-restraints excluded: chain F3 residue 49 ILE Chi-restraints excluded: chain F3 residue 68 ILE Chi-restraints excluded: chain F3 residue 100 VAL Chi-restraints excluded: chain F3 residue 124 LEU Chi-restraints excluded: chain F3 residue 235 ARG Chi-restraints excluded: chain G3 residue 139 VAL Chi-restraints excluded: chain G3 residue 155 TYR Chi-restraints excluded: chain G3 residue 217 ILE Chi-restraints excluded: chain G3 residue 300 VAL Chi-restraints excluded: chain G3 residue 316 THR Chi-restraints excluded: chain H3 residue 16 VAL Chi-restraints excluded: chain H3 residue 58 ASP Chi-restraints excluded: chain H3 residue 138 GLN Chi-restraints excluded: chain H3 residue 151 ILE Chi-restraints excluded: chain I3 residue 31 ILE Chi-restraints excluded: chain I3 residue 63 GLU Chi-restraints excluded: chain I3 residue 73 ASN Chi-restraints excluded: chain I3 residue 213 HIS Chi-restraints excluded: chain J3 residue 22 LEU Chi-restraints excluded: chain J3 residue 26 VAL Chi-restraints excluded: chain J3 residue 44 THR Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 67 HIS Chi-restraints excluded: chain M3 residue 30 VAL Chi-restraints excluded: chain M3 residue 43 THR Chi-restraints excluded: chain M3 residue 69 ARG Chi-restraints excluded: chain M3 residue 83 ASN Chi-restraints excluded: chain N3 residue 27 CYS Chi-restraints excluded: chain N3 residue 66 VAL Chi-restraints excluded: chain N3 residue 125 SER Chi-restraints excluded: chain N3 residue 126 THR Chi-restraints excluded: chain N3 residue 135 ILE Chi-restraints excluded: chain N3 residue 174 LEU Chi-restraints excluded: chain O3 residue 117 ARG Chi-restraints excluded: chain P3 residue 2 VAL Chi-restraints excluded: chain P3 residue 40 HIS Chi-restraints excluded: chain P3 residue 57 CYS Chi-restraints excluded: chain P3 residue 95 LEU Chi-restraints excluded: chain P3 residue 113 VAL Chi-restraints excluded: chain Q3 residue 81 VAL Chi-restraints excluded: chain Q3 residue 101 CYS Chi-restraints excluded: chain R3 residue 31 GLU Chi-restraints excluded: chain R3 residue 41 ILE Chi-restraints excluded: chain R3 residue 46 LYS Chi-restraints excluded: chain R3 residue 51 ILE Chi-restraints excluded: chain R3 residue 78 ILE Chi-restraints excluded: chain S3 residue 54 MET Chi-restraints excluded: chain S3 residue 150 ILE Chi-restraints excluded: chain S3 residue 152 PHE Chi-restraints excluded: chain T3 residue 2 THR Chi-restraints excluded: chain T3 residue 96 ILE Chi-restraints excluded: chain T3 residue 101 SER Chi-restraints excluded: chain T3 residue 106 LEU Chi-restraints excluded: chain U3 residue 103 VAL Chi-restraints excluded: chain W3 residue 5 LEU Chi-restraints excluded: chain W3 residue 41 LEU Chi-restraints excluded: chain X3 residue 127 LEU Chi-restraints excluded: chain Y3 residue 49 ILE Chi-restraints excluded: chain Y3 residue 79 VAL Chi-restraints excluded: chain Y3 residue 82 ILE Chi-restraints excluded: chain Y3 residue 88 GLU Chi-restraints excluded: chain Y3 residue 93 THR Chi-restraints excluded: chain Z3 residue 77 TYR Chi-restraints excluded: chain Z3 residue 85 TYR Chi-restraints excluded: chain Z3 residue 129 TRP Chi-restraints excluded: chain a3 residue 12 ARG Chi-restraints excluded: chain a3 residue 58 MET Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain b3 residue 8 THR Chi-restraints excluded: chain c3 residue 38 ILE Chi-restraints excluded: chain d3 residue 80 VAL Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain g3 residue 15 THR Chi-restraints excluded: chain g3 residue 48 VAL Chi-restraints excluded: chain h3 residue 44 LEU Chi-restraints excluded: chain h3 residue 47 ILE Chi-restraints excluded: chain h3 residue 82 ASP Chi-restraints excluded: chain h3 residue 88 THR Chi-restraints excluded: chain i3 residue 53 TYR Chi-restraints excluded: chain i3 residue 77 VAL Chi-restraints excluded: chain j3 residue 30 GLN Chi-restraints excluded: chain j3 residue 46 LYS Chi-restraints excluded: chain j3 residue 82 THR Chi-restraints excluded: chain k3 residue 36 VAL Chi-restraints excluded: chain k3 residue 44 THR Chi-restraints excluded: chain o3 residue 24 THR Chi-restraints excluded: chain o3 residue 90 HIS Chi-restraints excluded: chain p3 residue 4 ARG Chi-restraints excluded: chain p3 residue 10 ILE Chi-restraints excluded: chain p3 residue 16 THR Chi-restraints excluded: chain p3 residue 77 VAL Chi-restraints excluded: chain r3 residue 95 HIS Chi-restraints excluded: chain r3 residue 96 MET Chi-restraints excluded: chain r3 residue 97 ILE Chi-restraints excluded: chain r3 residue 103 HIS Chi-restraints excluded: chain r3 residue 115 SER Chi-restraints excluded: chain s3 residue 53 VAL Chi-restraints excluded: chain t3 residue 12 VAL Chi-restraints excluded: chain t3 residue 68 GLN Chi-restraints excluded: chain t3 residue 103 ASN Chi-restraints excluded: chain TT residue 92 GLN Chi-restraints excluded: chain TT residue 123 THR Chi-restraints excluded: chain TT residue 168 VAL Chi-restraints excluded: chain TT residue 174 CYS Chi-restraints excluded: chain TT residue 277 LEU Chi-restraints excluded: chain TT residue 293 LEU Chi-restraints excluded: chain TT residue 358 TYR Chi-restraints excluded: chain TT residue 386 ILE Chi-restraints excluded: chain TT residue 396 THR Chi-restraints excluded: chain TT residue 422 VAL Chi-restraints excluded: chain 1 residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 358 optimal weight: 0.9990 chunk 960 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 625 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 1067 optimal weight: 8.9990 chunk 885 optimal weight: 4.9990 chunk 494 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 353 optimal weight: 0.7980 chunk 560 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3 83 HIS A3 187 HIS A3 205 ASN ** B3 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 43 ASN C3 85 HIS ** C3 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 321 ASN ** D3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 63 GLN D3 122 GLN ** D3 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 287 HIS ** F3 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 99 GLN ** G3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 73 ASN I3 177 ASN ** J3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J3 112 HIS M3 70 GLN ** N3 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O3 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P3 80 GLN ** P3 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 7 HIS S3 50 GLN S3 125 GLN ** T3 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3 69 GLN T3 77 ASN ** T3 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3 131 GLN W3 17 HIS ** W3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y3 100 HIS ** a3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 89 ASN ** b3 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c3 19 GLN ** e3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f3 78 HIS ** h3 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j3 13 ASN ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r3 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TT 92 GLN ** TT 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4040 moved from start: 1.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 153762 Z= 0.249 Angle : 0.821 20.117 226397 Z= 0.412 Chirality : 0.043 0.369 28203 Planarity : 0.007 0.132 14170 Dihedral : 25.630 179.965 69964 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.34 % Rotamer: Outliers : 4.12 % Allowed : 22.95 % Favored : 72.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.09), residues: 7271 helix: -1.16 (0.10), residues: 2358 sheet: -2.19 (0.16), residues: 922 loop : -2.06 (0.09), residues: 3991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRPT3 125 HIS 0.026 0.002 HISA3 139 PHE 0.041 0.003 PHEF3 121 TYR 0.073 0.003 TYRW3 11 ARG 0.031 0.001 ARGW3 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 696 time to evaluate : 6.628 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: A3 176 ASP cc_start: 0.0581 (OUTLIER) cc_final: 0.0286 (m-30) REVERT: A3 227 ARG cc_start: -0.0939 (OUTLIER) cc_final: -0.1601 (ttm-80) REVERT: B3 168 MET cc_start: 0.3531 (mmt) cc_final: 0.2406 (mmp) REVERT: C3 100 ARG cc_start: 0.3625 (OUTLIER) cc_final: 0.3421 (tpt170) REVERT: C3 266 THR cc_start: 0.6976 (t) cc_final: 0.6480 (p) REVERT: C3 322 LEU cc_start: 0.4733 (tp) cc_final: 0.4222 (mp) REVERT: E3 217 ASP cc_start: 0.5181 (p0) cc_final: 0.4538 (m-30) REVERT: E3 263 LYS cc_start: 0.6734 (tptp) cc_final: 0.5579 (pttm) REVERT: E3 291 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.6162 (p90) REVERT: F3 63 MET cc_start: 0.7181 (mtt) cc_final: 0.6924 (mtm) REVERT: F3 162 ASN cc_start: 0.7627 (t0) cc_final: 0.7399 (t0) REVERT: G3 217 ILE cc_start: 0.0782 (OUTLIER) cc_final: 0.0286 (mp) REVERT: G3 230 MET cc_start: 0.3241 (mmp) cc_final: 0.0929 (mmp) REVERT: H3 20 LEU cc_start: 0.2063 (OUTLIER) cc_final: 0.1739 (pp) REVERT: H3 120 GLU cc_start: 0.3195 (pt0) cc_final: 0.2759 (mm-30) REVERT: I3 34 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7128 (t80) REVERT: I3 184 MET cc_start: 0.6656 (mmm) cc_final: 0.6331 (tpp) REVERT: I3 208 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8285 (mmtt) REVERT: J3 15 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8299 (tp) REVERT: M3 27 ILE cc_start: 0.8945 (mt) cc_final: 0.8742 (mt) REVERT: M3 60 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5299 (t80) REVERT: M3 104 MET cc_start: 0.4298 (mmp) cc_final: 0.2611 (tmm) REVERT: M3 118 MET cc_start: -0.2464 (mmm) cc_final: -0.2905 (mmm) REVERT: N3 195 ARG cc_start: 0.2662 (mtm-85) cc_final: 0.0721 (mmm160) REVERT: O3 105 PHE cc_start: 0.0309 (OUTLIER) cc_final: -0.0287 (m-80) REVERT: P3 148 MET cc_start: 0.2122 (ppp) cc_final: 0.1894 (ppp) REVERT: Q3 67 ILE cc_start: 0.5903 (mm) cc_final: 0.5469 (mm) REVERT: Q3 170 LYS cc_start: 0.8401 (ptmt) cc_final: 0.8076 (ttmt) REVERT: R3 31 GLU cc_start: 0.2386 (OUTLIER) cc_final: 0.0470 (tt0) REVERT: R3 41 ILE cc_start: -0.0130 (OUTLIER) cc_final: -0.0693 (tt) REVERT: R3 46 LYS cc_start: 0.1276 (OUTLIER) cc_final: 0.0544 (pttt) REVERT: R3 139 MET cc_start: 0.2207 (ttp) cc_final: 0.1177 (ttt) REVERT: S3 1 MET cc_start: 0.6294 (mmm) cc_final: 0.4352 (tpt) REVERT: S3 60 GLU cc_start: 0.7119 (pt0) cc_final: 0.6871 (pt0) REVERT: S3 93 MET cc_start: 0.7816 (mtm) cc_final: 0.7022 (mtm) REVERT: S3 125 GLN cc_start: 0.8202 (tt0) cc_final: 0.7981 (tt0) REVERT: T3 38 ASP cc_start: 0.7231 (m-30) cc_final: 0.6921 (m-30) REVERT: U3 34 MET cc_start: 0.2064 (tpp) cc_final: 0.1425 (tpp) REVERT: W3 1 MET cc_start: 0.2997 (tpp) cc_final: -0.1015 (tpt) REVERT: Y3 89 LYS cc_start: 0.5727 (mmtm) cc_final: 0.4596 (tmtt) REVERT: Z3 57 MET cc_start: 0.3221 (ttt) cc_final: 0.2713 (ttt) REVERT: b3 14 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7055 (mtt90) REVERT: b3 91 ARG cc_start: 0.6707 (mmp80) cc_final: 0.5474 (mtt90) REVERT: d3 57 MET cc_start: 0.0498 (mmt) cc_final: -0.0099 (mmt) REVERT: e3 90 MET cc_start: 0.4795 (tmm) cc_final: 0.4500 (tpt) REVERT: h3 44 LEU cc_start: 0.2456 (OUTLIER) cc_final: 0.2120 (pp) REVERT: i3 89 GLU cc_start: 0.5284 (OUTLIER) cc_final: 0.4799 (pp20) REVERT: j3 68 LYS cc_start: 0.0512 (OUTLIER) cc_final: -0.0179 (mmtp) REVERT: m3 68 MET cc_start: 0.7088 (mtt) cc_final: 0.6713 (mtt) REVERT: m3 92 THR cc_start: 0.7635 (p) cc_final: 0.7281 (p) REVERT: s3 55 MET cc_start: 0.2592 (ttm) cc_final: 0.2216 (ttm) REVERT: s3 85 ASN cc_start: 0.1830 (t0) cc_final: 0.1494 (m-40) REVERT: t3 85 LEU cc_start: 0.1954 (OUTLIER) cc_final: 0.1689 (pp) REVERT: NA 80 MET cc_start: 0.4065 (mtm) cc_final: 0.3756 (mtt) REVERT: TT 106 MET cc_start: -0.0174 (ptt) cc_final: -0.1714 (tmm) REVERT: TT 143 LYS cc_start: 0.2911 (mmmm) cc_final: 0.2217 (pttt) REVERT: TT 184 ASN cc_start: 0.3795 (t0) cc_final: 0.2714 (p0) REVERT: TT 286 GLU cc_start: 0.2177 (OUTLIER) cc_final: 0.1713 (tt0) REVERT: TT 371 LYS cc_start: 0.2801 (ttpt) cc_final: 0.0496 (tptp) outliers start: 260 outliers final: 130 residues processed: 903 average time/residue: 1.3200 time to fit residues: 2035.4884 Evaluate side-chains 735 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 587 time to evaluate : 6.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A3 residue 6 ARG Chi-restraints excluded: chain A3 residue 20 VAL Chi-restraints excluded: chain A3 residue 47 ASP Chi-restraints excluded: chain A3 residue 112 ILE Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 165 VAL Chi-restraints excluded: chain A3 residue 176 ASP Chi-restraints excluded: chain A3 residue 227 ARG Chi-restraints excluded: chain B3 residue 21 ARG Chi-restraints excluded: chain B3 residue 57 VAL Chi-restraints excluded: chain B3 residue 89 ILE Chi-restraints excluded: chain B3 residue 146 LEU Chi-restraints excluded: chain B3 residue 165 HIS Chi-restraints excluded: chain B3 residue 207 VAL Chi-restraints excluded: chain B3 residue 217 ILE Chi-restraints excluded: chain B3 residue 287 ILE Chi-restraints excluded: chain B3 residue 302 ASN Chi-restraints excluded: chain B3 residue 331 VAL Chi-restraints excluded: chain B3 residue 381 THR Chi-restraints excluded: chain C3 residue 47 ASN Chi-restraints excluded: chain C3 residue 100 ARG Chi-restraints excluded: chain C3 residue 101 MET Chi-restraints excluded: chain C3 residue 147 VAL Chi-restraints excluded: chain C3 residue 276 ASN Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain E3 residue 96 THR Chi-restraints excluded: chain E3 residue 140 VAL Chi-restraints excluded: chain E3 residue 159 ARG Chi-restraints excluded: chain E3 residue 291 PHE Chi-restraints excluded: chain F3 residue 242 LEU Chi-restraints excluded: chain G3 residue 155 TYR Chi-restraints excluded: chain G3 residue 217 ILE Chi-restraints excluded: chain G3 residue 300 VAL Chi-restraints excluded: chain G3 residue 313 GLU Chi-restraints excluded: chain G3 residue 316 THR Chi-restraints excluded: chain H3 residue 12 ILE Chi-restraints excluded: chain H3 residue 20 LEU Chi-restraints excluded: chain H3 residue 123 ILE Chi-restraints excluded: chain H3 residue 186 THR Chi-restraints excluded: chain I3 residue 31 ILE Chi-restraints excluded: chain I3 residue 34 PHE Chi-restraints excluded: chain I3 residue 212 LEU Chi-restraints excluded: chain J3 residue 15 LEU Chi-restraints excluded: chain J3 residue 34 THR Chi-restraints excluded: chain J3 residue 46 GLN Chi-restraints excluded: chain J3 residue 55 TYR Chi-restraints excluded: chain L3 residue 14 PHE Chi-restraints excluded: chain L3 residue 60 ARG Chi-restraints excluded: chain L3 residue 64 VAL Chi-restraints excluded: chain L3 residue 67 HIS Chi-restraints excluded: chain L3 residue 164 GLU Chi-restraints excluded: chain M3 residue 43 THR Chi-restraints excluded: chain M3 residue 60 PHE Chi-restraints excluded: chain M3 residue 62 LEU Chi-restraints excluded: chain M3 residue 83 ASN Chi-restraints excluded: chain N3 residue 66 VAL Chi-restraints excluded: chain N3 residue 125 SER Chi-restraints excluded: chain N3 residue 174 LEU Chi-restraints excluded: chain O3 residue 42 ASN Chi-restraints excluded: chain O3 residue 105 PHE Chi-restraints excluded: chain O3 residue 126 VAL Chi-restraints excluded: chain P3 residue 40 HIS Chi-restraints excluded: chain P3 residue 57 CYS Chi-restraints excluded: chain P3 residue 113 VAL Chi-restraints excluded: chain Q3 residue 42 THR Chi-restraints excluded: chain Q3 residue 63 LEU Chi-restraints excluded: chain Q3 residue 83 VAL Chi-restraints excluded: chain Q3 residue 101 CYS Chi-restraints excluded: chain R3 residue 25 ASP Chi-restraints excluded: chain R3 residue 31 GLU Chi-restraints excluded: chain R3 residue 41 ILE Chi-restraints excluded: chain R3 residue 46 LYS Chi-restraints excluded: chain R3 residue 51 ILE Chi-restraints excluded: chain R3 residue 78 ILE Chi-restraints excluded: chain R3 residue 125 LEU Chi-restraints excluded: chain S3 residue 150 ILE Chi-restraints excluded: chain S3 residue 166 ARG Chi-restraints excluded: chain T3 residue 2 THR Chi-restraints excluded: chain T3 residue 96 ILE Chi-restraints excluded: chain T3 residue 109 VAL Chi-restraints excluded: chain T3 residue 124 THR Chi-restraints excluded: chain T3 residue 128 LEU Chi-restraints excluded: chain U3 residue 103 VAL Chi-restraints excluded: chain V3 residue 60 MET Chi-restraints excluded: chain X3 residue 52 LEU Chi-restraints excluded: chain X3 residue 82 THR Chi-restraints excluded: chain Y3 residue 79 VAL Chi-restraints excluded: chain Y3 residue 82 ILE Chi-restraints excluded: chain Y3 residue 88 GLU Chi-restraints excluded: chain Y3 residue 93 THR Chi-restraints excluded: chain Z3 residue 77 TYR Chi-restraints excluded: chain Z3 residue 85 TYR Chi-restraints excluded: chain Z3 residue 129 TRP Chi-restraints excluded: chain a3 residue 101 ILE Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain b3 residue 8 THR Chi-restraints excluded: chain b3 residue 10 HIS Chi-restraints excluded: chain c3 residue 38 ILE Chi-restraints excluded: chain d3 residue 80 VAL Chi-restraints excluded: chain d3 residue 84 ILE Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain d3 residue 100 ASN Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain g3 residue 15 THR Chi-restraints excluded: chain g3 residue 32 TYR Chi-restraints excluded: chain g3 residue 48 VAL Chi-restraints excluded: chain h3 residue 44 LEU Chi-restraints excluded: chain h3 residue 82 ASP Chi-restraints excluded: chain h3 residue 88 THR Chi-restraints excluded: chain h3 residue 119 TYR Chi-restraints excluded: chain i3 residue 53 TYR Chi-restraints excluded: chain i3 residue 77 VAL Chi-restraints excluded: chain i3 residue 89 GLU Chi-restraints excluded: chain j3 residue 13 ASN Chi-restraints excluded: chain j3 residue 46 LYS Chi-restraints excluded: chain j3 residue 48 ASN Chi-restraints excluded: chain j3 residue 68 LYS Chi-restraints excluded: chain j3 residue 82 THR Chi-restraints excluded: chain k3 residue 8 ILE Chi-restraints excluded: chain k3 residue 36 VAL Chi-restraints excluded: chain k3 residue 44 THR Chi-restraints excluded: chain o3 residue 24 THR Chi-restraints excluded: chain p3 residue 16 THR Chi-restraints excluded: chain p3 residue 73 THR Chi-restraints excluded: chain p3 residue 77 VAL Chi-restraints excluded: chain p3 residue 83 ILE Chi-restraints excluded: chain r3 residue 4 HIS Chi-restraints excluded: chain r3 residue 20 ARG Chi-restraints excluded: chain r3 residue 27 THR Chi-restraints excluded: chain r3 residue 37 SER Chi-restraints excluded: chain r3 residue 43 LEU Chi-restraints excluded: chain r3 residue 96 MET Chi-restraints excluded: chain s3 residue 53 VAL Chi-restraints excluded: chain s3 residue 143 ILE Chi-restraints excluded: chain t3 residue 12 VAL Chi-restraints excluded: chain t3 residue 85 LEU Chi-restraints excluded: chain TT residue 68 LEU Chi-restraints excluded: chain TT residue 123 THR Chi-restraints excluded: chain TT residue 168 VAL Chi-restraints excluded: chain TT residue 174 CYS Chi-restraints excluded: chain TT residue 245 THR Chi-restraints excluded: chain TT residue 286 GLU Chi-restraints excluded: chain TT residue 293 LEU Chi-restraints excluded: chain TT residue 342 LEU Chi-restraints excluded: chain TT residue 358 TYR Chi-restraints excluded: chain TT residue 386 ILE Chi-restraints excluded: chain TT residue 422 VAL Chi-restraints excluded: chain TT residue 451 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 1028 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 608 optimal weight: 4.9990 chunk 779 optimal weight: 6.9990 chunk 603 optimal weight: 0.0970 chunk 898 optimal weight: 3.9990 chunk 595 optimal weight: 6.9990 chunk 1063 optimal weight: 2.9990 chunk 665 optimal weight: 7.9990 chunk 648 optimal weight: 5.9990 chunk 490 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 132 ASN A3 209 HIS ** B3 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 179 HIS ** B3 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 289 GLN ** C3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 39 GLN D3 122 GLN D3 282 GLN F3 55 HIS ** F3 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3 98 HIS ** I3 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 112 GLN ** I3 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3 23 ASN J3 71 HIS ** L3 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N3 32 GLN ** N3 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 108 GLN T3 3 ASN V3 77 HIS ** W3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y3 65 GLN ** a3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 41 HIS a3 74 ASN b3 10 HIS b3 50 ASN b3 61 ASN ** c3 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c3 72 HIS e3 52 GLN ** e3 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l3 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o3 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o3 18 HIS ** r3 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 95 HIS ** s3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s3 139 GLN ** s3 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TT 92 GLN ** TT 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 184 ASN ** TT 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 1.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.216 153762 Z= 0.442 Angle : 1.165 20.354 226397 Z= 0.581 Chirality : 0.057 0.829 28203 Planarity : 0.009 0.136 14170 Dihedral : 26.228 179.927 69963 Min Nonbonded Distance : 0.800 Molprobity Statistics. All-atom Clashscore : 33.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.83 % Favored : 90.03 % Rotamer: Outliers : 5.38 % Allowed : 22.86 % Favored : 71.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.09), residues: 7271 helix: -1.69 (0.10), residues: 2304 sheet: -2.25 (0.17), residues: 853 loop : -2.48 (0.09), residues: 4114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRPC3 111 HIS 0.026 0.003 HISW3 17 PHE 0.051 0.004 PHEB3 379 TYR 0.071 0.004 TYRE3 65 ARG 0.055 0.002 ARGp3 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 912 time to evaluate : 6.678 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: A3 108 PRO cc_start: 0.6256 (Cg_endo) cc_final: 0.5905 (Cg_exo) REVERT: A3 118 GLU cc_start: 0.4027 (OUTLIER) cc_final: 0.3407 (pt0) REVERT: A3 227 ARG cc_start: 0.0311 (OUTLIER) cc_final: -0.0087 (ttm-80) REVERT: B3 25 HIS cc_start: 0.2031 (OUTLIER) cc_final: 0.1241 (t70) REVERT: B3 216 MET cc_start: 0.0591 (tmm) cc_final: -0.0486 (ttm) REVERT: B3 261 ARG cc_start: 0.3197 (OUTLIER) cc_final: 0.1302 (mpp-170) REVERT: B3 271 GLN cc_start: 0.3641 (OUTLIER) cc_final: 0.2827 (tt0) REVERT: B3 294 LYS cc_start: 0.3281 (pttt) cc_final: 0.1991 (ttmt) REVERT: C3 75 ARG cc_start: 0.2720 (OUTLIER) cc_final: -0.0704 (ttp80) REVERT: C3 100 ARG cc_start: 0.4830 (OUTLIER) cc_final: 0.4146 (tpt-90) REVERT: C3 306 ARG cc_start: 0.8144 (mpp80) cc_final: 0.7942 (mpp80) REVERT: C3 310 HIS cc_start: 0.2842 (m90) cc_final: 0.2166 (m90) REVERT: C3 320 LYS cc_start: 0.6961 (mtpt) cc_final: 0.6626 (pttt) REVERT: D3 5 LYS cc_start: 0.8169 (tptt) cc_final: 0.7669 (tptp) REVERT: D3 9 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8329 (p0) REVERT: D3 128 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: D3 188 LYS cc_start: 0.7899 (mttp) cc_final: 0.7467 (pttm) REVERT: D3 225 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: D3 236 MET cc_start: 0.8529 (mmm) cc_final: 0.8178 (mmm) REVERT: E3 253 GLN cc_start: 0.3319 (OUTLIER) cc_final: 0.2264 (mp10) REVERT: F3 63 MET cc_start: 0.7874 (mtt) cc_final: 0.7574 (mtm) REVERT: F3 109 GLN cc_start: 0.7176 (pt0) cc_final: 0.6868 (tp40) REVERT: F3 136 GLU cc_start: 0.7821 (tt0) cc_final: 0.7209 (tt0) REVERT: F3 163 LYS cc_start: 0.8900 (mttp) cc_final: 0.8486 (mtmm) REVERT: F3 188 ASP cc_start: 0.7650 (t0) cc_final: 0.7348 (t0) REVERT: F3 247 ASN cc_start: 0.7983 (t0) cc_final: 0.7650 (t0) REVERT: H3 20 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4677 (pp) REVERT: H3 113 GLU cc_start: 0.4577 (mt-10) cc_final: 0.4205 (mt-10) REVERT: H3 128 MET cc_start: 0.3191 (tpp) cc_final: 0.2865 (tpp) REVERT: I3 34 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7862 (t80) REVERT: I3 38 ARG cc_start: 0.8277 (tpt-90) cc_final: 0.8065 (tpt-90) REVERT: I3 78 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7146 (mtmm) REVERT: I3 189 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8173 (mtp85) REVERT: I3 203 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7112 (mtt90) REVERT: I3 208 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8545 (mtpp) REVERT: J3 16 ARG cc_start: 0.7440 (mtm180) cc_final: 0.6939 (ptt90) REVERT: J3 22 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8819 (mt) REVERT: L3 190 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7891 (ttp-170) REVERT: L3 200 LYS cc_start: 0.7004 (mmmm) cc_final: 0.6660 (tmmt) REVERT: M3 34 ASN cc_start: 0.8469 (p0) cc_final: 0.8079 (p0) REVERT: M3 44 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7702 (mmm160) REVERT: M3 60 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6077 (t80) REVERT: M3 104 MET cc_start: 0.5500 (mmp) cc_final: 0.5246 (mmm) REVERT: O3 63 ASN cc_start: 0.3870 (OUTLIER) cc_final: 0.3593 (p0) REVERT: O3 105 PHE cc_start: 0.0931 (OUTLIER) cc_final: 0.0620 (m-10) REVERT: O3 182 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7209 (tp30) REVERT: P3 118 GLN cc_start: 0.5257 (mm-40) cc_final: 0.3898 (pt0) REVERT: Q3 17 GLU cc_start: 0.2570 (OUTLIER) cc_final: 0.2069 (pt0) REVERT: Q3 91 ARG cc_start: 0.4287 (OUTLIER) cc_final: 0.3211 (ptt-90) REVERT: Q3 125 GLN cc_start: 0.8223 (mt0) cc_final: 0.7999 (mt0) REVERT: Q3 172 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.8308 (tmm160) REVERT: R3 7 GLN cc_start: 0.1720 (OUTLIER) cc_final: 0.0898 (mp-120) REVERT: R3 41 ILE cc_start: -0.0487 (OUTLIER) cc_final: -0.1208 (tt) REVERT: R3 46 LYS cc_start: 0.0932 (OUTLIER) cc_final: -0.0020 (pttt) REVERT: R3 89 MET cc_start: 0.1772 (mmm) cc_final: 0.1105 (tpt) REVERT: R3 139 MET cc_start: 0.2443 (ttp) cc_final: 0.1642 (ttt) REVERT: S3 10 TYR cc_start: 0.8355 (m-80) cc_final: 0.8144 (m-80) REVERT: S3 77 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8915 (p0) REVERT: T3 38 ASP cc_start: 0.7585 (m-30) cc_final: 0.7114 (m-30) REVERT: T3 83 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8295 (pttm) REVERT: T3 114 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7880 (tm-30) REVERT: W3 1 MET cc_start: 0.3794 (tpp) cc_final: -0.0081 (tpt) REVERT: Z3 57 MET cc_start: 0.2972 (ttt) cc_final: 0.2416 (ttt) REVERT: Z3 131 PHE cc_start: 0.2700 (m-80) cc_final: 0.1243 (m-80) REVERT: b3 57 MET cc_start: 0.5661 (OUTLIER) cc_final: 0.5276 (mmm) REVERT: b3 95 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.7332 (ttp80) REVERT: e3 20 PHE cc_start: 0.1102 (OUTLIER) cc_final: 0.0503 (t80) REVERT: e3 48 ARG cc_start: -0.0188 (OUTLIER) cc_final: -0.0423 (mtm-85) REVERT: f3 106 TYR cc_start: 0.4652 (OUTLIER) cc_final: 0.3960 (p90) REVERT: i3 3 LEU cc_start: 0.6326 (mt) cc_final: 0.5876 (mp) REVERT: i3 7 MET cc_start: 0.3297 (OUTLIER) cc_final: 0.2969 (mtt) REVERT: i3 89 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6023 (pp20) REVERT: j3 47 TYR cc_start: 0.2203 (OUTLIER) cc_final: 0.0384 (m-80) REVERT: j3 79 ARG cc_start: 0.4130 (OUTLIER) cc_final: 0.3410 (ttp-170) REVERT: j3 85 LYS cc_start: 0.5236 (mppt) cc_final: 0.4716 (mppt) REVERT: l3 25 GLN cc_start: 0.3588 (OUTLIER) cc_final: 0.1664 (mp10) REVERT: o3 27 LYS cc_start: 0.8259 (mptt) cc_final: 0.8012 (mtmm) REVERT: p3 61 MET cc_start: 0.3928 (tpp) cc_final: 0.3447 (tpt) REVERT: s3 45 MET cc_start: 0.4137 (mmm) cc_final: 0.3903 (mmm) REVERT: s3 55 MET cc_start: 0.2942 (ttm) cc_final: 0.2380 (ttm) REVERT: s3 61 MET cc_start: 0.0071 (ptp) cc_final: -0.0243 (ptp) REVERT: s3 177 MET cc_start: 0.3662 (tmm) cc_final: 0.3255 (tpt) REVERT: t3 87 GLU cc_start: 0.3235 (OUTLIER) cc_final: 0.2456 (mm-30) REVERT: NA 80 MET cc_start: 0.4601 (mtm) cc_final: 0.4268 (mtt) REVERT: NB 102 MET cc_start: -0.0990 (mtm) cc_final: -0.2025 (mmt) REVERT: TT 106 MET cc_start: -0.0905 (ptt) cc_final: -0.1523 (tmm) REVERT: TT 143 LYS cc_start: 0.3366 (mmmm) cc_final: 0.2931 (pttt) REVERT: TT 286 GLU cc_start: 0.1960 (OUTLIER) cc_final: 0.1458 (tt0) outliers start: 340 outliers final: 158 residues processed: 1173 average time/residue: 1.3127 time to fit residues: 2605.7076 Evaluate side-chains 929 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 737 time to evaluate : 6.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A3 residue 47 ASP Chi-restraints excluded: chain A3 residue 118 GLU Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 154 SER Chi-restraints excluded: chain A3 residue 165 VAL Chi-restraints excluded: chain A3 residue 227 ARG Chi-restraints excluded: chain B3 residue 21 ARG Chi-restraints excluded: chain B3 residue 25 HIS Chi-restraints excluded: chain B3 residue 57 VAL Chi-restraints excluded: chain B3 residue 89 ILE Chi-restraints excluded: chain B3 residue 123 HIS Chi-restraints excluded: chain B3 residue 146 LEU Chi-restraints excluded: chain B3 residue 153 MET Chi-restraints excluded: chain B3 residue 165 HIS Chi-restraints excluded: chain B3 residue 171 LEU Chi-restraints excluded: chain B3 residue 217 ILE Chi-restraints excluded: chain B3 residue 248 LEU Chi-restraints excluded: chain B3 residue 254 ILE Chi-restraints excluded: chain B3 residue 261 ARG Chi-restraints excluded: chain B3 residue 262 VAL Chi-restraints excluded: chain B3 residue 271 GLN Chi-restraints excluded: chain B3 residue 287 ILE Chi-restraints excluded: chain B3 residue 299 ILE Chi-restraints excluded: chain B3 residue 302 ASN Chi-restraints excluded: chain B3 residue 313 SER Chi-restraints excluded: chain B3 residue 331 VAL Chi-restraints excluded: chain B3 residue 347 LEU Chi-restraints excluded: chain B3 residue 381 THR Chi-restraints excluded: chain C3 residue 57 LEU Chi-restraints excluded: chain C3 residue 75 ARG Chi-restraints excluded: chain C3 residue 76 ILE Chi-restraints excluded: chain C3 residue 100 ARG Chi-restraints excluded: chain C3 residue 113 ARG Chi-restraints excluded: chain C3 residue 219 LYS Chi-restraints excluded: chain C3 residue 276 ASN Chi-restraints excluded: chain C3 residue 281 MET Chi-restraints excluded: chain D3 residue 9 ASN Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain D3 residue 128 ASP Chi-restraints excluded: chain D3 residue 225 GLN Chi-restraints excluded: chain D3 residue 234 ASP Chi-restraints excluded: chain E3 residue 56 ILE Chi-restraints excluded: chain E3 residue 140 VAL Chi-restraints excluded: chain E3 residue 155 ILE Chi-restraints excluded: chain E3 residue 160 HIS Chi-restraints excluded: chain E3 residue 253 GLN Chi-restraints excluded: chain E3 residue 287 HIS Chi-restraints excluded: chain F3 residue 213 SER Chi-restraints excluded: chain G3 residue 155 TYR Chi-restraints excluded: chain G3 residue 198 THR Chi-restraints excluded: chain G3 residue 313 GLU Chi-restraints excluded: chain G3 residue 316 THR Chi-restraints excluded: chain H3 residue 20 LEU Chi-restraints excluded: chain H3 residue 57 VAL Chi-restraints excluded: chain H3 residue 186 THR Chi-restraints excluded: chain I3 residue 34 PHE Chi-restraints excluded: chain I3 residue 43 VAL Chi-restraints excluded: chain I3 residue 148 VAL Chi-restraints excluded: chain I3 residue 197 VAL Chi-restraints excluded: chain J3 residue 22 LEU Chi-restraints excluded: chain J3 residue 34 THR Chi-restraints excluded: chain J3 residue 39 VAL Chi-restraints excluded: chain J3 residue 55 TYR Chi-restraints excluded: chain J3 residue 132 VAL Chi-restraints excluded: chain L3 residue 14 PHE Chi-restraints excluded: chain L3 residue 60 ARG Chi-restraints excluded: chain L3 residue 64 VAL Chi-restraints excluded: chain L3 residue 67 HIS Chi-restraints excluded: chain L3 residue 142 GLU Chi-restraints excluded: chain L3 residue 150 LEU Chi-restraints excluded: chain M3 residue 38 VAL Chi-restraints excluded: chain M3 residue 60 PHE Chi-restraints excluded: chain M3 residue 62 LEU Chi-restraints excluded: chain M3 residue 69 ARG Chi-restraints excluded: chain M3 residue 83 ASN Chi-restraints excluded: chain N3 residue 27 CYS Chi-restraints excluded: chain N3 residue 66 VAL Chi-restraints excluded: chain N3 residue 75 VAL Chi-restraints excluded: chain N3 residue 125 SER Chi-restraints excluded: chain N3 residue 151 ILE Chi-restraints excluded: chain N3 residue 174 LEU Chi-restraints excluded: chain O3 residue 42 ASN Chi-restraints excluded: chain O3 residue 63 ASN Chi-restraints excluded: chain O3 residue 105 PHE Chi-restraints excluded: chain O3 residue 117 ARG Chi-restraints excluded: chain O3 residue 190 SER Chi-restraints excluded: chain P3 residue 2 VAL Chi-restraints excluded: chain P3 residue 40 HIS Chi-restraints excluded: chain P3 residue 57 CYS Chi-restraints excluded: chain P3 residue 70 CYS Chi-restraints excluded: chain P3 residue 113 VAL Chi-restraints excluded: chain P3 residue 140 MET Chi-restraints excluded: chain Q3 residue 17 GLU Chi-restraints excluded: chain Q3 residue 75 ARG Chi-restraints excluded: chain Q3 residue 91 ARG Chi-restraints excluded: chain Q3 residue 101 CYS Chi-restraints excluded: chain R3 residue 7 GLN Chi-restraints excluded: chain R3 residue 25 ASP Chi-restraints excluded: chain R3 residue 41 ILE Chi-restraints excluded: chain R3 residue 46 LYS Chi-restraints excluded: chain R3 residue 51 ILE Chi-restraints excluded: chain R3 residue 78 ILE Chi-restraints excluded: chain R3 residue 95 TRP Chi-restraints excluded: chain S3 residue 75 VAL Chi-restraints excluded: chain S3 residue 77 ASN Chi-restraints excluded: chain S3 residue 150 ILE Chi-restraints excluded: chain S3 residue 166 ARG Chi-restraints excluded: chain T3 residue 2 THR Chi-restraints excluded: chain T3 residue 159 MET Chi-restraints excluded: chain U3 residue 103 VAL Chi-restraints excluded: chain V3 residue 22 VAL Chi-restraints excluded: chain V3 residue 60 MET Chi-restraints excluded: chain W3 residue 5 LEU Chi-restraints excluded: chain Y3 residue 82 ILE Chi-restraints excluded: chain Y3 residue 88 GLU Chi-restraints excluded: chain Y3 residue 93 THR Chi-restraints excluded: chain Y3 residue 105 VAL Chi-restraints excluded: chain Z3 residue 54 THR Chi-restraints excluded: chain Z3 residue 85 TYR Chi-restraints excluded: chain Z3 residue 96 VAL Chi-restraints excluded: chain Z3 residue 129 TRP Chi-restraints excluded: chain a3 residue 56 VAL Chi-restraints excluded: chain a3 residue 69 PHE Chi-restraints excluded: chain a3 residue 72 THR Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain b3 residue 8 THR Chi-restraints excluded: chain b3 residue 57 MET Chi-restraints excluded: chain c3 residue 38 ILE Chi-restraints excluded: chain d3 residue 46 LEU Chi-restraints excluded: chain d3 residue 77 ILE Chi-restraints excluded: chain d3 residue 80 VAL Chi-restraints excluded: chain d3 residue 84 ILE Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain d3 residue 95 ASP Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain e3 residue 20 PHE Chi-restraints excluded: chain e3 residue 48 ARG Chi-restraints excluded: chain e3 residue 96 CYS Chi-restraints excluded: chain e3 residue 111 ILE Chi-restraints excluded: chain f3 residue 30 ILE Chi-restraints excluded: chain f3 residue 33 VAL Chi-restraints excluded: chain f3 residue 106 TYR Chi-restraints excluded: chain g3 residue 5 LEU Chi-restraints excluded: chain g3 residue 11 LEU Chi-restraints excluded: chain g3 residue 15 THR Chi-restraints excluded: chain g3 residue 65 MET Chi-restraints excluded: chain h3 residue 54 ILE Chi-restraints excluded: chain h3 residue 82 ASP Chi-restraints excluded: chain h3 residue 119 TYR Chi-restraints excluded: chain i3 residue 7 MET Chi-restraints excluded: chain i3 residue 19 LYS Chi-restraints excluded: chain i3 residue 53 TYR Chi-restraints excluded: chain i3 residue 89 GLU Chi-restraints excluded: chain j3 residue 45 ARG Chi-restraints excluded: chain j3 residue 46 LYS Chi-restraints excluded: chain j3 residue 47 TYR Chi-restraints excluded: chain j3 residue 48 ASN Chi-restraints excluded: chain j3 residue 49 TRP Chi-restraints excluded: chain j3 residue 79 ARG Chi-restraints excluded: chain j3 residue 82 THR Chi-restraints excluded: chain k3 residue 28 ASN Chi-restraints excluded: chain k3 residue 36 VAL Chi-restraints excluded: chain k3 residue 44 THR Chi-restraints excluded: chain l3 residue 25 GLN Chi-restraints excluded: chain o3 residue 24 THR Chi-restraints excluded: chain p3 residue 16 THR Chi-restraints excluded: chain p3 residue 83 ILE Chi-restraints excluded: chain r3 residue 4 HIS Chi-restraints excluded: chain r3 residue 20 ARG Chi-restraints excluded: chain r3 residue 27 THR Chi-restraints excluded: chain r3 residue 35 ARG Chi-restraints excluded: chain r3 residue 37 SER Chi-restraints excluded: chain r3 residue 95 HIS Chi-restraints excluded: chain r3 residue 101 LYS Chi-restraints excluded: chain s3 residue 35 VAL Chi-restraints excluded: chain s3 residue 53 VAL Chi-restraints excluded: chain s3 residue 71 ASN Chi-restraints excluded: chain t3 residue 12 VAL Chi-restraints excluded: chain t3 residue 87 GLU Chi-restraints excluded: chain TT residue 68 LEU Chi-restraints excluded: chain TT residue 123 THR Chi-restraints excluded: chain TT residue 168 VAL Chi-restraints excluded: chain TT residue 245 THR Chi-restraints excluded: chain TT residue 286 GLU Chi-restraints excluded: chain TT residue 293 LEU Chi-restraints excluded: chain TT residue 333 VAL Chi-restraints excluded: chain TT residue 344 SER Chi-restraints excluded: chain TT residue 358 TYR Chi-restraints excluded: chain TT residue 386 ILE Chi-restraints excluded: chain TT residue 422 VAL Chi-restraints excluded: chain TT residue 451 ASP Chi-restraints excluded: chain 1 residue 61 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 657 optimal weight: 9.9990 chunk 424 optimal weight: 0.9980 chunk 634 optimal weight: 0.0970 chunk 320 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 205 optimal weight: 0.9990 chunk 675 optimal weight: 3.9990 chunk 724 optimal weight: 6.9990 chunk 525 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 835 optimal weight: 6.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3 162 ASN B3 55 HIS ** B3 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 245 HIS ** C3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 100 ASN I3 213 HIS J3 10 ASN J3 65 ASN J3 104 ASN ** J3 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3 111 GLN ** O3 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O3 96 GLN ** O3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 116 HIS Q3 77 ASN ** R3 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 125 GLN T3 22 HIS T3 49 GLN T3 66 ASN T3 95 HIS ** W3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y3 65 GLN Y3 72 GLN ** a3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 93 ASN a3 120 GLN ** e3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e3 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h3 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p3 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r3 21 ASN r3 23 GLN r3 95 HIS ** s3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TT 92 GLN TT 156 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4717 moved from start: 1.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 153762 Z= 0.191 Angle : 0.734 15.426 226397 Z= 0.370 Chirality : 0.040 0.434 28203 Planarity : 0.006 0.070 14170 Dihedral : 25.620 179.541 69961 Min Nonbonded Distance : 1.004 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.71 % Favored : 94.25 % Rotamer: Outliers : 2.74 % Allowed : 25.15 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.49 (0.09), residues: 7271 helix: -0.83 (0.10), residues: 2323 sheet: -2.12 (0.16), residues: 924 loop : -2.06 (0.09), residues: 4024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRPT3 125 HIS 0.014 0.001 HISH3 76 PHE 0.023 0.002 PHEZ3 71 TYR 0.029 0.002 TYRY3 78 ARG 0.023 0.001 ARGr3 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 815 time to evaluate : 6.718 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: B3 216 MET cc_start: 0.0493 (tmm) cc_final: -0.0834 (ttm) REVERT: B3 294 LYS cc_start: 0.3108 (pttt) cc_final: 0.1567 (ttmt) REVERT: C3 196 MET cc_start: 0.0718 (mmm) cc_final: 0.0245 (mpp) REVERT: D3 5 LYS cc_start: 0.8058 (tptt) cc_final: 0.7558 (tptp) REVERT: F3 42 ARG cc_start: 0.5432 (mtm-85) cc_final: 0.5220 (tmm160) REVERT: F3 70 MET cc_start: 0.8284 (tpp) cc_final: 0.7834 (mmt) REVERT: F3 150 ASN cc_start: 0.8739 (m-40) cc_final: 0.8520 (m-40) REVERT: F3 162 ASN cc_start: 0.8604 (t0) cc_final: 0.8387 (t0) REVERT: F3 163 LYS cc_start: 0.8886 (mttp) cc_final: 0.8514 (mtmm) REVERT: F3 246 MET cc_start: 0.7802 (tpp) cc_final: 0.7525 (tpp) REVERT: G3 102 ARG cc_start: 0.4041 (mmt180) cc_final: 0.3379 (mmm160) REVERT: G3 278 ASN cc_start: 0.5831 (t0) cc_final: 0.5395 (t0) REVERT: G3 283 TYR cc_start: 0.5456 (t80) cc_final: 0.4508 (t80) REVERT: H3 120 GLU cc_start: 0.4974 (mp0) cc_final: 0.4408 (tt0) REVERT: H3 128 MET cc_start: 0.3017 (tpp) cc_final: 0.2342 (tpp) REVERT: I3 34 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7935 (t80) REVERT: I3 78 LYS cc_start: 0.7518 (ttmm) cc_final: 0.7035 (mtmm) REVERT: I3 102 MET cc_start: 0.6514 (mmt) cc_final: 0.6298 (mmm) REVERT: I3 203 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.6718 (mtt90) REVERT: I3 208 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8495 (mtpp) REVERT: J3 41 GLU cc_start: 0.7355 (tp30) cc_final: 0.6613 (tp30) REVERT: J3 52 LYS cc_start: 0.7871 (mttp) cc_final: 0.7613 (mttt) REVERT: M3 34 ASN cc_start: 0.8517 (p0) cc_final: 0.7988 (p0) REVERT: M3 118 MET cc_start: -0.1565 (mmm) cc_final: -0.1875 (mmm) REVERT: P3 118 GLN cc_start: 0.4533 (mm-40) cc_final: 0.3538 (pt0) REVERT: Q3 64 SER cc_start: 0.9271 (p) cc_final: 0.8820 (p) REVERT: Q3 91 ARG cc_start: 0.4568 (ptt-90) cc_final: 0.3928 (ptt-90) REVERT: Q3 125 GLN cc_start: 0.8342 (mt0) cc_final: 0.7901 (mt0) REVERT: R3 41 ILE cc_start: -0.0895 (OUTLIER) cc_final: -0.1402 (tt) REVERT: R3 89 MET cc_start: 0.2881 (mmm) cc_final: 0.2025 (tpt) REVERT: R3 139 MET cc_start: 0.1968 (ttp) cc_final: 0.1031 (ttt) REVERT: S3 28 TYR cc_start: 0.8748 (m-80) cc_final: 0.8420 (m-10) REVERT: S3 77 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.7839 (p0) REVERT: T3 38 ASP cc_start: 0.7630 (m-30) cc_final: 0.7138 (m-30) REVERT: T3 114 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7709 (tm-30) REVERT: T3 127 GLN cc_start: 0.8154 (tp40) cc_final: 0.7934 (tp-100) REVERT: V3 14 PHE cc_start: 0.1649 (OUTLIER) cc_final: 0.0504 (t80) REVERT: W3 1 MET cc_start: 0.3962 (tpp) cc_final: 0.0017 (tpt) REVERT: Z3 57 MET cc_start: 0.2977 (ttt) cc_final: 0.2598 (ttt) REVERT: d3 46 LEU cc_start: 0.0338 (OUTLIER) cc_final: -0.0031 (mm) REVERT: e3 20 PHE cc_start: 0.0611 (OUTLIER) cc_final: 0.0052 (t80) REVERT: e3 90 MET cc_start: 0.5638 (tpt) cc_final: 0.5228 (tpt) REVERT: f3 106 TYR cc_start: 0.3949 (OUTLIER) cc_final: 0.3346 (p90) REVERT: h3 25 LYS cc_start: 0.3461 (pttm) cc_final: 0.2776 (pttm) REVERT: i3 3 LEU cc_start: 0.6449 (mt) cc_final: 0.6152 (mp) REVERT: i3 7 MET cc_start: 0.4004 (mtt) cc_final: 0.3665 (mtt) REVERT: i3 21 VAL cc_start: 0.3021 (m) cc_final: 0.2787 (m) REVERT: i3 94 LEU cc_start: 0.6344 (tt) cc_final: 0.6121 (tp) REVERT: j3 85 LYS cc_start: 0.5203 (mppt) cc_final: 0.4629 (mppt) REVERT: m3 87 LYS cc_start: 0.8341 (tttt) cc_final: 0.8000 (ttmm) REVERT: o3 27 LYS cc_start: 0.8210 (mptt) cc_final: 0.7962 (mttm) REVERT: s3 47 LEU cc_start: 0.4685 (mt) cc_final: 0.4263 (mm) REVERT: s3 55 MET cc_start: 0.3226 (ttm) cc_final: 0.2884 (ttm) REVERT: NA 80 MET cc_start: 0.4371 (mtm) cc_final: 0.4053 (mtt) REVERT: TT 90 ARG cc_start: 0.3449 (mtt90) cc_final: 0.2418 (ttt90) REVERT: TT 106 MET cc_start: -0.0680 (ptt) cc_final: -0.1649 (tmm) REVERT: TT 143 LYS cc_start: 0.3149 (mmmm) cc_final: 0.2771 (pttt) REVERT: TT 193 MET cc_start: 0.1503 (ptt) cc_final: 0.0966 (ptt) REVERT: 1 1 MET cc_start: 0.2319 (mtm) cc_final: 0.1397 (mtm) outliers start: 173 outliers final: 111 residues processed: 941 average time/residue: 1.3065 time to fit residues: 2117.9491 Evaluate side-chains 834 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 716 time to evaluate : 6.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A3 residue 20 VAL Chi-restraints excluded: chain A3 residue 47 ASP Chi-restraints excluded: chain A3 residue 112 ILE Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 154 SER Chi-restraints excluded: chain A3 residue 162 ASN Chi-restraints excluded: chain A3 residue 165 VAL Chi-restraints excluded: chain A3 residue 207 VAL Chi-restraints excluded: chain B3 residue 89 ILE Chi-restraints excluded: chain B3 residue 123 HIS Chi-restraints excluded: chain B3 residue 153 MET Chi-restraints excluded: chain B3 residue 217 ILE Chi-restraints excluded: chain B3 residue 299 ILE Chi-restraints excluded: chain B3 residue 331 VAL Chi-restraints excluded: chain B3 residue 381 THR Chi-restraints excluded: chain C3 residue 76 ILE Chi-restraints excluded: chain C3 residue 101 MET Chi-restraints excluded: chain C3 residue 237 ILE Chi-restraints excluded: chain C3 residue 281 MET Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain D3 residue 267 ASN Chi-restraints excluded: chain E3 residue 176 LEU Chi-restraints excluded: chain E3 residue 291 PHE Chi-restraints excluded: chain F3 residue 213 SER Chi-restraints excluded: chain G3 residue 155 TYR Chi-restraints excluded: chain H3 residue 12 ILE Chi-restraints excluded: chain H3 residue 26 ILE Chi-restraints excluded: chain H3 residue 57 VAL Chi-restraints excluded: chain I3 residue 34 PHE Chi-restraints excluded: chain I3 residue 43 VAL Chi-restraints excluded: chain I3 residue 148 VAL Chi-restraints excluded: chain I3 residue 197 VAL Chi-restraints excluded: chain I3 residue 212 LEU Chi-restraints excluded: chain J3 residue 55 TYR Chi-restraints excluded: chain J3 residue 73 THR Chi-restraints excluded: chain J3 residue 158 SER Chi-restraints excluded: chain L3 residue 14 PHE Chi-restraints excluded: chain L3 residue 67 HIS Chi-restraints excluded: chain L3 residue 86 ILE Chi-restraints excluded: chain M3 residue 38 VAL Chi-restraints excluded: chain M3 residue 62 LEU Chi-restraints excluded: chain M3 residue 78 GLU Chi-restraints excluded: chain M3 residue 83 ASN Chi-restraints excluded: chain N3 residue 125 SER Chi-restraints excluded: chain N3 residue 174 LEU Chi-restraints excluded: chain O3 residue 42 ASN Chi-restraints excluded: chain O3 residue 108 ILE Chi-restraints excluded: chain P3 residue 2 VAL Chi-restraints excluded: chain P3 residue 94 MET Chi-restraints excluded: chain P3 residue 113 VAL Chi-restraints excluded: chain Q3 residue 42 THR Chi-restraints excluded: chain Q3 residue 77 ASN Chi-restraints excluded: chain Q3 residue 83 VAL Chi-restraints excluded: chain R3 residue 41 ILE Chi-restraints excluded: chain R3 residue 46 LYS Chi-restraints excluded: chain R3 residue 78 ILE Chi-restraints excluded: chain R3 residue 109 TYR Chi-restraints excluded: chain R3 residue 125 LEU Chi-restraints excluded: chain S3 residue 75 VAL Chi-restraints excluded: chain S3 residue 77 ASN Chi-restraints excluded: chain S3 residue 123 SER Chi-restraints excluded: chain S3 residue 166 ARG Chi-restraints excluded: chain T3 residue 4 THR Chi-restraints excluded: chain U3 residue 103 VAL Chi-restraints excluded: chain V3 residue 14 PHE Chi-restraints excluded: chain V3 residue 22 VAL Chi-restraints excluded: chain X3 residue 100 VAL Chi-restraints excluded: chain Y3 residue 72 GLN Chi-restraints excluded: chain Y3 residue 82 ILE Chi-restraints excluded: chain Y3 residue 88 GLU Chi-restraints excluded: chain Y3 residue 93 THR Chi-restraints excluded: chain Z3 residue 85 TYR Chi-restraints excluded: chain Z3 residue 129 TRP Chi-restraints excluded: chain a3 residue 56 VAL Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain b3 residue 8 THR Chi-restraints excluded: chain c3 residue 19 GLN Chi-restraints excluded: chain d3 residue 46 LEU Chi-restraints excluded: chain d3 residue 80 VAL Chi-restraints excluded: chain d3 residue 84 ILE Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain e3 residue 20 PHE Chi-restraints excluded: chain e3 residue 99 ILE Chi-restraints excluded: chain f3 residue 28 LEU Chi-restraints excluded: chain f3 residue 75 THR Chi-restraints excluded: chain f3 residue 106 TYR Chi-restraints excluded: chain g3 residue 15 THR Chi-restraints excluded: chain g3 residue 48 VAL Chi-restraints excluded: chain h3 residue 119 TYR Chi-restraints excluded: chain i3 residue 9 VAL Chi-restraints excluded: chain j3 residue 33 THR Chi-restraints excluded: chain j3 residue 46 LYS Chi-restraints excluded: chain j3 residue 48 ASN Chi-restraints excluded: chain j3 residue 61 THR Chi-restraints excluded: chain j3 residue 82 THR Chi-restraints excluded: chain k3 residue 8 ILE Chi-restraints excluded: chain k3 residue 28 ASN Chi-restraints excluded: chain o3 residue 98 LYS Chi-restraints excluded: chain p3 residue 83 ILE Chi-restraints excluded: chain r3 residue 4 HIS Chi-restraints excluded: chain r3 residue 7 TRP Chi-restraints excluded: chain r3 residue 27 THR Chi-restraints excluded: chain r3 residue 97 ILE Chi-restraints excluded: chain s3 residue 53 VAL Chi-restraints excluded: chain s3 residue 71 ASN Chi-restraints excluded: chain s3 residue 143 ILE Chi-restraints excluded: chain TT residue 68 LEU Chi-restraints excluded: chain TT residue 123 THR Chi-restraints excluded: chain TT residue 168 VAL Chi-restraints excluded: chain TT residue 245 THR Chi-restraints excluded: chain TT residue 293 LEU Chi-restraints excluded: chain TT residue 358 TYR Chi-restraints excluded: chain TT residue 386 ILE Chi-restraints excluded: chain TT residue 387 LEU Chi-restraints excluded: chain TT residue 396 THR Chi-restraints excluded: chain TT residue 422 VAL Chi-restraints excluded: chain 1 residue 61 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 967 optimal weight: 4.9990 chunk 1018 optimal weight: 6.9990 chunk 929 optimal weight: 10.0000 chunk 990 optimal weight: 6.9990 chunk 596 optimal weight: 0.6980 chunk 431 optimal weight: 5.9990 chunk 777 optimal weight: 9.9990 chunk 304 optimal weight: 0.8980 chunk 895 optimal weight: 10.0000 chunk 936 optimal weight: 20.0000 chunk 987 optimal weight: 7.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3 22 HIS ** A3 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 55 HIS ** B3 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 245 HIS B3 376 HIS ** C3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E3 194 GLN ** E3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 57 HIS F3 98 ASN F3 150 ASN ** G3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 153 HIS H3 8 GLN H3 76 HIS H3 98 HIS H3 102 ASN ** I3 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3 98 ASN J3 104 ASN ** L3 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 188 ASN ** N3 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N3 158 HIS ** P3 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 40 ASN ** Q3 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R3 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3 49 GLN T3 69 GLN ** T3 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W3 17 HIS ** W3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y3 20 ASN Y3 65 GLN a3 19 HIS ** a3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 74 ASN a3 85 GLN a3 120 GLN b3 50 ASN ** c3 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e3 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g3 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i3 20 ASN j3 13 ASN ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 100 ASN ** s3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TT 423 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 1.9360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.212 153762 Z= 0.520 Angle : 1.285 18.166 226397 Z= 0.636 Chirality : 0.061 0.529 28203 Planarity : 0.010 0.211 14170 Dihedral : 26.339 179.889 69960 Min Nonbonded Distance : 0.896 Molprobity Statistics. All-atom Clashscore : 36.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.54 % Favored : 88.14 % Rotamer: Outliers : 3.74 % Allowed : 24.99 % Favored : 71.27 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.09), residues: 7271 helix: -1.60 (0.10), residues: 2291 sheet: -2.32 (0.16), residues: 847 loop : -2.56 (0.09), residues: 4133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.006 TRPR3 95 HIS 0.023 0.004 HISr3 4 PHE 0.076 0.005 PHEY3 3 TYR 0.068 0.005 TYRT3 57 ARG 0.026 0.002 ARGA3 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 917 time to evaluate : 9.049 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: B3 216 MET cc_start: 0.1390 (tmm) cc_final: 0.0729 (tmm) REVERT: B3 271 GLN cc_start: 0.3115 (OUTLIER) cc_final: 0.2279 (tt0) REVERT: B3 294 LYS cc_start: 0.3918 (pttt) cc_final: 0.2450 (ttmt) REVERT: C3 121 ARG cc_start: 0.5065 (mtt180) cc_final: 0.4326 (mtm180) REVERT: C3 254 GLU cc_start: 0.5201 (pm20) cc_final: 0.4877 (tp30) REVERT: C3 350 ARG cc_start: 0.7745 (mtt180) cc_final: 0.6669 (mtm180) REVERT: D3 5 LYS cc_start: 0.8305 (tptt) cc_final: 0.7794 (tptp) REVERT: D3 9 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8147 (p0) REVERT: D3 58 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7603 (ttm-80) REVERT: D3 183 TYR cc_start: 0.7864 (t80) cc_final: 0.7509 (t80) REVERT: D3 225 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8357 (mp10) REVERT: D3 237 GLU cc_start: 0.7272 (tp30) cc_final: 0.6977 (tp30) REVERT: E3 64 MET cc_start: 0.8744 (tpp) cc_final: 0.8223 (tpt) REVERT: E3 114 LYS cc_start: 0.4824 (mtpt) cc_final: 0.4485 (mtpt) REVERT: E3 140 VAL cc_start: -0.0935 (OUTLIER) cc_final: -0.1446 (t) REVERT: E3 159 ARG cc_start: 0.5232 (ptm160) cc_final: 0.4695 (ptm-80) REVERT: E3 271 GLN cc_start: 0.8145 (pt0) cc_final: 0.7927 (pm20) REVERT: F3 40 MET cc_start: 0.6919 (tmm) cc_final: 0.6498 (tmm) REVERT: F3 70 MET cc_start: 0.8582 (tpp) cc_final: 0.7780 (mmt) REVERT: F3 163 LYS cc_start: 0.8880 (mttp) cc_final: 0.8393 (mtmm) REVERT: F3 213 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8154 (t) REVERT: F3 231 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: G3 102 ARG cc_start: 0.4708 (mmt180) cc_final: 0.4212 (mmp-170) REVERT: G3 198 THR cc_start: 0.7060 (t) cc_final: 0.6548 (m) REVERT: G3 278 ASN cc_start: 0.7300 (t0) cc_final: 0.6832 (t0) REVERT: H3 1 MET cc_start: 0.2171 (tmm) cc_final: 0.1649 (ttp) REVERT: H3 41 ILE cc_start: 0.6166 (mm) cc_final: 0.5850 (mm) REVERT: H3 64 ARG cc_start: 0.7233 (mtp-110) cc_final: 0.6985 (ttm170) REVERT: H3 128 MET cc_start: 0.3768 (tpp) cc_final: 0.3284 (tpp) REVERT: I3 121 LYS cc_start: 0.8316 (ttmm) cc_final: 0.8064 (mmtp) REVERT: I3 203 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: J3 12 MET cc_start: 0.8231 (mmm) cc_final: 0.7735 (mmm) REVERT: L3 8 MET cc_start: 0.2852 (mmt) cc_final: 0.1954 (mmt) REVERT: L3 200 LYS cc_start: 0.7737 (mmmm) cc_final: 0.7462 (tmmt) REVERT: M3 54 CYS cc_start: 0.8502 (p) cc_final: 0.8275 (p) REVERT: M3 118 MET cc_start: 0.0904 (mmm) cc_final: 0.0452 (tpp) REVERT: N3 73 ARG cc_start: 0.2755 (ttm-80) cc_final: 0.1622 (ttm-80) REVERT: O3 93 LYS cc_start: 0.8278 (mttm) cc_final: 0.7796 (mmmm) REVERT: O3 182 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7095 (tp30) REVERT: P3 39 MET cc_start: 0.5798 (tmm) cc_final: 0.3270 (mtp) REVERT: P3 62 ARG cc_start: 0.7576 (ttm170) cc_final: 0.5632 (mtt-85) REVERT: P3 76 TRP cc_start: 0.7092 (m100) cc_final: 0.6869 (m100) REVERT: P3 118 GLN cc_start: 0.5626 (mm-40) cc_final: 0.3556 (pt0) REVERT: Q3 17 GLU cc_start: 0.2379 (OUTLIER) cc_final: 0.2003 (pt0) REVERT: Q3 26 ARG cc_start: 0.6336 (mtt-85) cc_final: 0.5885 (tpp80) REVERT: Q3 64 SER cc_start: 0.9446 (p) cc_final: 0.8926 (p) REVERT: Q3 91 ARG cc_start: 0.4049 (OUTLIER) cc_final: 0.3847 (ptt-90) REVERT: Q3 125 GLN cc_start: 0.8396 (mt0) cc_final: 0.7993 (mt0) REVERT: Q3 154 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8308 (mtpp) REVERT: R3 41 ILE cc_start: -0.0725 (OUTLIER) cc_final: -0.1382 (tt) REVERT: R3 139 MET cc_start: 0.2581 (ttp) cc_final: 0.1808 (ttt) REVERT: S3 50 GLN cc_start: 0.8167 (mt0) cc_final: 0.7908 (tt0) REVERT: S3 77 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8018 (p0) REVERT: S3 139 ARG cc_start: 0.6226 (mmt180) cc_final: 0.4552 (mpt180) REVERT: T3 38 ASP cc_start: 0.7597 (m-30) cc_final: 0.7002 (m-30) REVERT: T3 114 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7646 (tm-30) REVERT: V3 14 PHE cc_start: 0.2297 (OUTLIER) cc_final: 0.1895 (t80) REVERT: W3 1 MET cc_start: 0.3869 (tpp) cc_final: -0.0037 (tpt) REVERT: Y3 11 ARG cc_start: 0.6590 (ttm170) cc_final: 0.5699 (ttt90) REVERT: Y3 125 SER cc_start: 0.2431 (OUTLIER) cc_final: 0.2198 (p) REVERT: Z3 18 TYR cc_start: 0.2662 (m-10) cc_final: 0.2076 (m-80) REVERT: Z3 57 MET cc_start: 0.2650 (ttt) cc_final: 0.2397 (ttt) REVERT: Z3 131 PHE cc_start: 0.2510 (m-80) cc_final: 0.1041 (m-80) REVERT: a3 12 ARG cc_start: 0.5775 (mtt-85) cc_final: 0.5565 (mmm-85) REVERT: a3 48 TYR cc_start: 0.4774 (m-80) cc_final: 0.4400 (m-80) REVERT: a3 85 GLN cc_start: 0.8656 (pt0) cc_final: 0.8390 (pt0) REVERT: a3 119 LYS cc_start: 0.8225 (mttt) cc_final: 0.7883 (mttp) REVERT: e3 9 LYS cc_start: 0.6097 (tppt) cc_final: 0.5868 (mmtt) REVERT: e3 20 PHE cc_start: 0.1618 (OUTLIER) cc_final: 0.1105 (t80) REVERT: e3 36 ARG cc_start: 0.7952 (mmp80) cc_final: 0.7722 (mmp-170) REVERT: e3 48 ARG cc_start: 0.2825 (OUTLIER) cc_final: 0.2001 (mtm-85) REVERT: f3 106 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.4421 (p90) REVERT: g3 32 TYR cc_start: 0.0635 (OUTLIER) cc_final: -0.0440 (t80) REVERT: i3 4 ARG cc_start: 0.6769 (mmp80) cc_final: 0.5820 (mtm180) REVERT: i3 46 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6870 (mm-30) REVERT: j3 13 ASN cc_start: 0.0358 (OUTLIER) cc_final: 0.0139 (p0) REVERT: j3 21 ARG cc_start: 0.5663 (ttm170) cc_final: 0.5408 (ptm160) REVERT: m3 87 LYS cc_start: 0.8522 (tttt) cc_final: 0.8204 (ttmm) REVERT: o3 3 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8245 (p0) REVERT: o3 58 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7077 (ttpp) REVERT: o3 102 GLN cc_start: 0.5708 (mm110) cc_final: 0.5391 (mt0) REVERT: r3 101 LYS cc_start: 0.8181 (mttp) cc_final: 0.7757 (mmtt) REVERT: s3 55 MET cc_start: 0.3153 (ttm) cc_final: 0.2771 (ttm) REVERT: t3 31 LYS cc_start: 0.1923 (OUTLIER) cc_final: 0.1355 (mppt) REVERT: t3 68 GLN cc_start: 0.3017 (OUTLIER) cc_final: 0.1517 (mp10) REVERT: NA 80 MET cc_start: 0.3961 (mtm) cc_final: 0.3702 (mtt) REVERT: TT 106 MET cc_start: -0.0812 (ptt) cc_final: -0.1493 (tmm) REVERT: TT 193 MET cc_start: 0.1193 (ptt) cc_final: 0.0913 (ptt) REVERT: TT 294 GLU cc_start: 0.4659 (tp30) cc_final: 0.4283 (mm-30) outliers start: 236 outliers final: 140 residues processed: 1085 average time/residue: 1.3336 time to fit residues: 2457.2770 Evaluate side-chains 989 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 828 time to evaluate : 6.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A3 residue 47 ASP Chi-restraints excluded: chain A3 residue 112 ILE Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 137 ILE Chi-restraints excluded: chain A3 residue 162 ASN Chi-restraints excluded: chain A3 residue 165 VAL Chi-restraints excluded: chain B3 residue 21 ARG Chi-restraints excluded: chain B3 residue 89 ILE Chi-restraints excluded: chain B3 residue 95 THR Chi-restraints excluded: chain B3 residue 153 MET Chi-restraints excluded: chain B3 residue 217 ILE Chi-restraints excluded: chain B3 residue 245 HIS Chi-restraints excluded: chain B3 residue 262 VAL Chi-restraints excluded: chain B3 residue 271 GLN Chi-restraints excluded: chain B3 residue 299 ILE Chi-restraints excluded: chain B3 residue 331 VAL Chi-restraints excluded: chain B3 residue 381 THR Chi-restraints excluded: chain C3 residue 22 VAL Chi-restraints excluded: chain C3 residue 76 ILE Chi-restraints excluded: chain C3 residue 107 THR Chi-restraints excluded: chain C3 residue 266 THR Chi-restraints excluded: chain C3 residue 281 MET Chi-restraints excluded: chain C3 residue 302 LEU Chi-restraints excluded: chain D3 residue 9 ASN Chi-restraints excluded: chain D3 residue 40 ASP Chi-restraints excluded: chain D3 residue 58 ARG Chi-restraints excluded: chain D3 residue 81 HIS Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain D3 residue 225 GLN Chi-restraints excluded: chain D3 residue 234 ASP Chi-restraints excluded: chain E3 residue 140 VAL Chi-restraints excluded: chain E3 residue 176 LEU Chi-restraints excluded: chain E3 residue 194 GLN Chi-restraints excluded: chain E3 residue 197 VAL Chi-restraints excluded: chain E3 residue 211 ILE Chi-restraints excluded: chain E3 residue 291 PHE Chi-restraints excluded: chain F3 residue 73 MET Chi-restraints excluded: chain F3 residue 129 ILE Chi-restraints excluded: chain F3 residue 172 THR Chi-restraints excluded: chain F3 residue 213 SER Chi-restraints excluded: chain F3 residue 231 ASP Chi-restraints excluded: chain G3 residue 155 TYR Chi-restraints excluded: chain G3 residue 313 GLU Chi-restraints excluded: chain G3 residue 316 THR Chi-restraints excluded: chain H3 residue 57 VAL Chi-restraints excluded: chain H3 residue 177 ASP Chi-restraints excluded: chain I3 residue 148 VAL Chi-restraints excluded: chain I3 residue 197 VAL Chi-restraints excluded: chain I3 residue 212 LEU Chi-restraints excluded: chain J3 residue 40 LEU Chi-restraints excluded: chain J3 residue 55 TYR Chi-restraints excluded: chain J3 residue 104 ASN Chi-restraints excluded: chain J3 residue 132 VAL Chi-restraints excluded: chain J3 residue 158 SER Chi-restraints excluded: chain L3 residue 14 PHE Chi-restraints excluded: chain L3 residue 60 ARG Chi-restraints excluded: chain L3 residue 67 HIS Chi-restraints excluded: chain L3 residue 164 GLU Chi-restraints excluded: chain M3 residue 6 PHE Chi-restraints excluded: chain M3 residue 62 LEU Chi-restraints excluded: chain M3 residue 78 GLU Chi-restraints excluded: chain N3 residue 66 VAL Chi-restraints excluded: chain N3 residue 151 ILE Chi-restraints excluded: chain O3 residue 42 ASN Chi-restraints excluded: chain O3 residue 108 ILE Chi-restraints excluded: chain P3 residue 113 VAL Chi-restraints excluded: chain P3 residue 140 MET Chi-restraints excluded: chain Q3 residue 17 GLU Chi-restraints excluded: chain Q3 residue 42 THR Chi-restraints excluded: chain Q3 residue 83 VAL Chi-restraints excluded: chain Q3 residue 91 ARG Chi-restraints excluded: chain Q3 residue 122 THR Chi-restraints excluded: chain Q3 residue 136 THR Chi-restraints excluded: chain Q3 residue 137 VAL Chi-restraints excluded: chain R3 residue 41 ILE Chi-restraints excluded: chain R3 residue 46 LYS Chi-restraints excluded: chain R3 residue 78 ILE Chi-restraints excluded: chain R3 residue 125 LEU Chi-restraints excluded: chain S3 residue 16 CYS Chi-restraints excluded: chain S3 residue 77 ASN Chi-restraints excluded: chain S3 residue 123 SER Chi-restraints excluded: chain S3 residue 132 ILE Chi-restraints excluded: chain S3 residue 166 ARG Chi-restraints excluded: chain T3 residue 2 THR Chi-restraints excluded: chain T3 residue 4 THR Chi-restraints excluded: chain T3 residue 40 VAL Chi-restraints excluded: chain T3 residue 93 ILE Chi-restraints excluded: chain U3 residue 103 VAL Chi-restraints excluded: chain V3 residue 14 PHE Chi-restraints excluded: chain V3 residue 22 VAL Chi-restraints excluded: chain V3 residue 60 MET Chi-restraints excluded: chain V3 residue 105 ILE Chi-restraints excluded: chain W3 residue 52 THR Chi-restraints excluded: chain Y3 residue 88 GLU Chi-restraints excluded: chain Y3 residue 93 THR Chi-restraints excluded: chain Y3 residue 125 SER Chi-restraints excluded: chain Z3 residue 74 VAL Chi-restraints excluded: chain Z3 residue 85 TYR Chi-restraints excluded: chain Z3 residue 129 TRP Chi-restraints excluded: chain a3 residue 8 THR Chi-restraints excluded: chain a3 residue 15 VAL Chi-restraints excluded: chain a3 residue 56 VAL Chi-restraints excluded: chain a3 residue 69 PHE Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain a3 residue 129 PHE Chi-restraints excluded: chain b3 residue 8 THR Chi-restraints excluded: chain c3 residue 19 GLN Chi-restraints excluded: chain d3 residue 46 LEU Chi-restraints excluded: chain d3 residue 84 ILE Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain d3 residue 95 ASP Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain e3 residue 20 PHE Chi-restraints excluded: chain e3 residue 26 ASP Chi-restraints excluded: chain e3 residue 29 VAL Chi-restraints excluded: chain e3 residue 48 ARG Chi-restraints excluded: chain e3 residue 53 ILE Chi-restraints excluded: chain e3 residue 96 CYS Chi-restraints excluded: chain e3 residue 99 ILE Chi-restraints excluded: chain f3 residue 75 THR Chi-restraints excluded: chain f3 residue 106 TYR Chi-restraints excluded: chain g3 residue 5 LEU Chi-restraints excluded: chain g3 residue 15 THR Chi-restraints excluded: chain g3 residue 32 TYR Chi-restraints excluded: chain g3 residue 48 VAL Chi-restraints excluded: chain g3 residue 65 MET Chi-restraints excluded: chain h3 residue 119 TYR Chi-restraints excluded: chain i3 residue 53 TYR Chi-restraints excluded: chain j3 residue 13 ASN Chi-restraints excluded: chain j3 residue 33 THR Chi-restraints excluded: chain j3 residue 48 ASN Chi-restraints excluded: chain j3 residue 82 THR Chi-restraints excluded: chain k3 residue 5 ILE Chi-restraints excluded: chain k3 residue 28 ASN Chi-restraints excluded: chain k3 residue 36 VAL Chi-restraints excluded: chain k3 residue 44 THR Chi-restraints excluded: chain m3 residue 92 THR Chi-restraints excluded: chain o3 residue 3 ASN Chi-restraints excluded: chain o3 residue 24 THR Chi-restraints excluded: chain o3 residue 98 LYS Chi-restraints excluded: chain p3 residue 73 THR Chi-restraints excluded: chain r3 residue 27 THR Chi-restraints excluded: chain s3 residue 12 ASN Chi-restraints excluded: chain s3 residue 53 VAL Chi-restraints excluded: chain s3 residue 71 ASN Chi-restraints excluded: chain s3 residue 143 ILE Chi-restraints excluded: chain t3 residue 31 LYS Chi-restraints excluded: chain t3 residue 68 GLN Chi-restraints excluded: chain TT residue 68 LEU Chi-restraints excluded: chain TT residue 123 THR Chi-restraints excluded: chain TT residue 168 VAL Chi-restraints excluded: chain TT residue 245 THR Chi-restraints excluded: chain TT residue 293 LEU Chi-restraints excluded: chain TT residue 344 SER Chi-restraints excluded: chain TT residue 358 TYR Chi-restraints excluded: chain TT residue 375 THR Chi-restraints excluded: chain TT residue 386 ILE Chi-restraints excluded: chain TT residue 387 LEU Chi-restraints excluded: chain TT residue 396 THR Chi-restraints excluded: chain TT residue 422 VAL Chi-restraints excluded: chain TT residue 451 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 650 optimal weight: 0.9990 chunk 1047 optimal weight: 4.9990 chunk 639 optimal weight: 0.0170 chunk 496 optimal weight: 5.9990 chunk 728 optimal weight: 20.0000 chunk 1098 optimal weight: 8.9990 chunk 1011 optimal weight: 5.9990 chunk 875 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 675 optimal weight: 2.9990 chunk 536 optimal weight: 0.6980 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3 38 HIS A3 162 ASN ** A3 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 245 HIS C3 38 ASN ** C3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 50 GLN ** C3 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 245 HIS ** C3 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 291 GLN ** E3 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E3 259 GLN F3 57 HIS ** F3 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 199 HIS ** G3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J3 65 ASN L3 19 GLN L3 149 GLN ** N3 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N3 201 HIS ** O3 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 40 ASN ** Q3 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3 49 GLN ** W3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y3 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 60 HIS a3 62 HIS a3 120 GLN c3 15 ASN ** c3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h3 62 ASN ** h3 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i3 20 ASN j3 13 ASN ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 36 ASN r3 41 ASN ** s3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5308 moved from start: 1.9260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 153762 Z= 0.222 Angle : 0.788 20.304 226397 Z= 0.397 Chirality : 0.042 0.472 28203 Planarity : 0.006 0.152 14170 Dihedral : 25.738 179.997 69960 Min Nonbonded Distance : 0.985 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.04 % Favored : 92.93 % Rotamer: Outliers : 2.25 % Allowed : 26.84 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.09), residues: 7271 helix: -0.95 (0.10), residues: 2341 sheet: -2.13 (0.16), residues: 889 loop : -2.20 (0.09), residues: 4041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRPR3 95 HIS 0.033 0.002 HISB3 245 PHE 0.028 0.002 PHEZ3 71 TYR 0.028 0.002 TYRO3 71 ARG 0.046 0.001 ARGB3 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14542 Ramachandran restraints generated. 7271 Oldfield, 0 Emsley, 7271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 876 time to evaluate : 6.751 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: B3 216 MET cc_start: 0.1611 (tmm) cc_final: 0.0861 (ttm) REVERT: B3 271 GLN cc_start: 0.1456 (OUTLIER) cc_final: -0.0637 (tt0) REVERT: B3 294 LYS cc_start: 0.3278 (pttt) cc_final: 0.2023 (ttmt) REVERT: C3 56 GLU cc_start: 0.6996 (mp0) cc_final: 0.6626 (mp0) REVERT: C3 196 MET cc_start: 0.0736 (mpp) cc_final: -0.1458 (mpp) REVERT: C3 350 ARG cc_start: 0.7623 (mtt180) cc_final: 0.6563 (mtm180) REVERT: D3 5 LYS cc_start: 0.8121 (tptt) cc_final: 0.7576 (tptp) REVERT: D3 183 TYR cc_start: 0.7845 (t80) cc_final: 0.7450 (t80) REVERT: E3 75 TYR cc_start: 0.3002 (m-80) cc_final: 0.1847 (p90) REVERT: E3 189 LEU cc_start: 0.8573 (mt) cc_final: 0.8198 (mt) REVERT: F3 70 MET cc_start: 0.8279 (tpp) cc_final: 0.7788 (mmt) REVERT: F3 163 LYS cc_start: 0.8810 (mttp) cc_final: 0.8353 (mtmm) REVERT: F3 246 MET cc_start: 0.8390 (tpp) cc_final: 0.8126 (tpp) REVERT: G3 102 ARG cc_start: 0.4284 (mmt180) cc_final: 0.3845 (mmt180) REVERT: G3 228 ARG cc_start: 0.8005 (tmt170) cc_final: 0.7740 (tpt170) REVERT: G3 278 ASN cc_start: 0.7343 (t0) cc_final: 0.6923 (t0) REVERT: H3 1 MET cc_start: 0.3285 (tmm) cc_final: 0.2831 (ttp) REVERT: H3 11 ASP cc_start: 0.8310 (m-30) cc_final: 0.8099 (m-30) REVERT: H3 67 LEU cc_start: 0.8871 (mt) cc_final: 0.8588 (mt) REVERT: I3 203 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7383 (mtm-85) REVERT: J3 65 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7465 (t0) REVERT: L3 19 GLN cc_start: 0.3153 (OUTLIER) cc_final: 0.2700 (mt0) REVERT: L3 60 ARG cc_start: 0.4777 (OUTLIER) cc_final: 0.4024 (ttm110) REVERT: L3 200 LYS cc_start: 0.7987 (mmmm) cc_final: 0.7675 (tmmt) REVERT: M3 34 ASN cc_start: 0.8579 (p0) cc_final: 0.8118 (p0) REVERT: N3 73 ARG cc_start: 0.1851 (ttm-80) cc_final: 0.1034 (ttm-80) REVERT: O3 26 GLN cc_start: 0.8649 (mm110) cc_final: 0.8300 (mm-40) REVERT: P3 39 MET cc_start: 0.5564 (tmm) cc_final: 0.3288 (mtp) REVERT: P3 76 TRP cc_start: 0.6904 (m100) cc_final: 0.6584 (m100) REVERT: P3 118 GLN cc_start: 0.5121 (mm-40) cc_final: 0.3572 (pt0) REVERT: Q3 64 SER cc_start: 0.9116 (p) cc_final: 0.8711 (p) REVERT: Q3 125 GLN cc_start: 0.8544 (mt0) cc_final: 0.8059 (mt0) REVERT: R3 41 ILE cc_start: -0.0959 (OUTLIER) cc_final: -0.1586 (tt) REVERT: R3 46 LYS cc_start: 0.1278 (OUTLIER) cc_final: -0.0420 (pttt) REVERT: R3 139 MET cc_start: 0.1951 (ttp) cc_final: 0.0792 (ttt) REVERT: S3 28 TYR cc_start: 0.8752 (m-80) cc_final: 0.8478 (m-10) REVERT: S3 50 GLN cc_start: 0.7985 (mt0) cc_final: 0.7751 (tt0) REVERT: S3 77 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8028 (p0) REVERT: S3 139 ARG cc_start: 0.5790 (mmt180) cc_final: 0.4775 (mmt180) REVERT: T3 157 GLU cc_start: 0.7524 (tt0) cc_final: 0.7038 (tm-30) REVERT: V3 14 PHE cc_start: 0.2289 (OUTLIER) cc_final: 0.1679 (t80) REVERT: W3 1 MET cc_start: 0.4224 (tpp) cc_final: 0.0057 (tpt) REVERT: a3 12 ARG cc_start: 0.5624 (mtt-85) cc_final: 0.5061 (mmm-85) REVERT: b3 57 MET cc_start: 0.6083 (mmp) cc_final: 0.5438 (mmp) REVERT: e3 20 PHE cc_start: 0.0980 (OUTLIER) cc_final: 0.0440 (t80) REVERT: g3 32 TYR cc_start: 0.0341 (OUTLIER) cc_final: -0.0643 (t80) REVERT: j3 64 MET cc_start: 0.6572 (mpp) cc_final: 0.6156 (mpp) REVERT: m3 87 LYS cc_start: 0.8421 (tttt) cc_final: 0.8044 (ttmm) REVERT: o3 58 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7271 (tttm) REVERT: r3 101 LYS cc_start: 0.8357 (mttp) cc_final: 0.7979 (mmtt) REVERT: r3 108 MET cc_start: 0.3705 (mpp) cc_final: 0.3248 (mpp) REVERT: s3 55 MET cc_start: 0.2894 (ttm) cc_final: 0.2653 (ttm) REVERT: t3 68 GLN cc_start: 0.2824 (OUTLIER) cc_final: 0.1487 (mp10) REVERT: TT 90 ARG cc_start: 0.3144 (mtt90) cc_final: 0.2444 (ttt90) REVERT: TT 106 MET cc_start: -0.0773 (ptt) cc_final: -0.1483 (tmm) REVERT: TT 193 MET cc_start: 0.1810 (ptt) cc_final: 0.1372 (ptt) REVERT: TT 472 GLN cc_start: 0.2555 (OUTLIER) cc_final: 0.0586 (mt0) outliers start: 142 outliers final: 95 residues processed: 976 average time/residue: 1.3369 time to fit residues: 2226.3333 Evaluate side-chains 918 residues out of total 6318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 811 time to evaluate : 6.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A3 residue 47 ASP Chi-restraints excluded: chain A3 residue 112 ILE Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 137 ILE Chi-restraints excluded: chain A3 residue 157 VAL Chi-restraints excluded: chain A3 residue 162 ASN Chi-restraints excluded: chain A3 residue 165 VAL Chi-restraints excluded: chain B3 residue 21 ARG Chi-restraints excluded: chain B3 residue 217 ILE Chi-restraints excluded: chain B3 residue 245 HIS Chi-restraints excluded: chain B3 residue 262 VAL Chi-restraints excluded: chain B3 residue 271 GLN Chi-restraints excluded: chain B3 residue 331 VAL Chi-restraints excluded: chain B3 residue 381 THR Chi-restraints excluded: chain C3 residue 76 ILE Chi-restraints excluded: chain D3 residue 40 ASP Chi-restraints excluded: chain D3 residue 118 ILE Chi-restraints excluded: chain E3 residue 176 LEU Chi-restraints excluded: chain E3 residue 197 VAL Chi-restraints excluded: chain E3 residue 211 ILE Chi-restraints excluded: chain F3 residue 62 GLN Chi-restraints excluded: chain F3 residue 73 MET Chi-restraints excluded: chain F3 residue 128 SER Chi-restraints excluded: chain G3 residue 155 TYR Chi-restraints excluded: chain H3 residue 57 VAL Chi-restraints excluded: chain I3 residue 197 VAL Chi-restraints excluded: chain I3 residue 212 LEU Chi-restraints excluded: chain J3 residue 39 VAL Chi-restraints excluded: chain J3 residue 55 TYR Chi-restraints excluded: chain J3 residue 65 ASN Chi-restraints excluded: chain J3 residue 73 THR Chi-restraints excluded: chain J3 residue 74 VAL Chi-restraints excluded: chain J3 residue 132 VAL Chi-restraints excluded: chain L3 residue 14 PHE Chi-restraints excluded: chain L3 residue 19 GLN Chi-restraints excluded: chain L3 residue 60 ARG Chi-restraints excluded: chain L3 residue 67 HIS Chi-restraints excluded: chain M3 residue 24 LEU Chi-restraints excluded: chain M3 residue 62 LEU Chi-restraints excluded: chain M3 residue 78 GLU Chi-restraints excluded: chain O3 residue 42 ASN Chi-restraints excluded: chain O3 residue 108 ILE Chi-restraints excluded: chain P3 residue 113 VAL Chi-restraints excluded: chain Q3 residue 42 THR Chi-restraints excluded: chain Q3 residue 76 GLU Chi-restraints excluded: chain Q3 residue 129 ASP Chi-restraints excluded: chain R3 residue 41 ILE Chi-restraints excluded: chain R3 residue 46 LYS Chi-restraints excluded: chain R3 residue 78 ILE Chi-restraints excluded: chain R3 residue 125 LEU Chi-restraints excluded: chain S3 residue 16 CYS Chi-restraints excluded: chain S3 residue 77 ASN Chi-restraints excluded: chain S3 residue 123 SER Chi-restraints excluded: chain S3 residue 132 ILE Chi-restraints excluded: chain T3 residue 4 THR Chi-restraints excluded: chain T3 residue 40 VAL Chi-restraints excluded: chain U3 residue 103 VAL Chi-restraints excluded: chain V3 residue 14 PHE Chi-restraints excluded: chain V3 residue 105 ILE Chi-restraints excluded: chain Y3 residue 88 GLU Chi-restraints excluded: chain Y3 residue 93 THR Chi-restraints excluded: chain Z3 residue 85 TYR Chi-restraints excluded: chain Z3 residue 129 TRP Chi-restraints excluded: chain a3 residue 8 THR Chi-restraints excluded: chain a3 residue 72 THR Chi-restraints excluded: chain a3 residue 122 VAL Chi-restraints excluded: chain c3 residue 19 GLN Chi-restraints excluded: chain d3 residue 46 LEU Chi-restraints excluded: chain d3 residue 84 ILE Chi-restraints excluded: chain d3 residue 86 VAL Chi-restraints excluded: chain d3 residue 103 TYR Chi-restraints excluded: chain e3 residue 20 PHE Chi-restraints excluded: chain e3 residue 29 VAL Chi-restraints excluded: chain e3 residue 99 ILE Chi-restraints excluded: chain g3 residue 15 THR Chi-restraints excluded: chain g3 residue 32 TYR Chi-restraints excluded: chain g3 residue 48 VAL Chi-restraints excluded: chain h3 residue 119 TYR Chi-restraints excluded: chain j3 residue 13 ASN Chi-restraints excluded: chain j3 residue 33 THR Chi-restraints excluded: chain j3 residue 82 THR Chi-restraints excluded: chain k3 residue 5 ILE Chi-restraints excluded: chain k3 residue 28 ASN Chi-restraints excluded: chain k3 residue 44 THR Chi-restraints excluded: chain m3 residue 92 THR Chi-restraints excluded: chain o3 residue 98 LYS Chi-restraints excluded: chain p3 residue 83 ILE Chi-restraints excluded: chain r3 residue 18 ILE Chi-restraints excluded: chain r3 residue 27 THR Chi-restraints excluded: chain r3 residue 97 ILE Chi-restraints excluded: chain s3 residue 47 LEU Chi-restraints excluded: chain s3 residue 53 VAL Chi-restraints excluded: chain s3 residue 71 ASN Chi-restraints excluded: chain s3 residue 143 ILE Chi-restraints excluded: chain t3 residue 68 GLN Chi-restraints excluded: chain TT residue 68 LEU Chi-restraints excluded: chain TT residue 123 THR Chi-restraints excluded: chain TT residue 168 VAL Chi-restraints excluded: chain TT residue 245 THR Chi-restraints excluded: chain TT residue 293 LEU Chi-restraints excluded: chain TT residue 358 TYR Chi-restraints excluded: chain TT residue 386 ILE Chi-restraints excluded: chain TT residue 387 LEU Chi-restraints excluded: chain TT residue 396 THR Chi-restraints excluded: chain TT residue 422 VAL Chi-restraints excluded: chain TT residue 472 GLN Chi-restraints excluded: chain 1 residue 61 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 695 optimal weight: 5.9990 chunk 932 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 chunk 806 optimal weight: 4.9990 chunk 129 optimal weight: 0.4980 chunk 243 optimal weight: 0.1980 chunk 876 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 899 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 245 HIS ** C3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 267 ASN ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 289 HIS H3 42 ASN I3 51 HIS ** I3 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I3 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I3 144 ASN L3 67 HIS ** N3 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O3 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q3 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U3 94 ASN ** W3 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y3 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 120 GLN b3 50 ASN ** c3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h3 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i3 20 ASN ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m3 61 GLN ** n3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 36 ASN ** s3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s3 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.252028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.234098 restraints weight = 252815.113| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 1.15 r_work: 0.4444 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 1.9619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 153762 Z= 0.232 Angle : 0.778 15.450 226397 Z= 0.392 Chirality : 0.041 0.412 28203 Planarity : 0.006 0.135 14170 Dihedral : 25.602 179.683 69960 Min Nonbonded Distance : 0.989 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.68 % Favored : 91.28 % Rotamer: Outliers : 2.06 % Allowed : 26.80 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.09), residues: 7271 helix: -0.67 (0.10), residues: 2352 sheet: -2.03 (0.16), residues: 870 loop : -2.09 (0.09), residues: 4049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRPR3 95 HIS 0.064 0.002 HISB3 245 PHE 0.029 0.002 PHEa3 129 TYR 0.037 0.002 TYRr3 25 ARG 0.060 0.001 ARGJ3 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31657.21 seconds wall clock time: 558 minutes 34.52 seconds (33514.52 seconds total)