Starting phenix.real_space_refine on Mon Mar 18 09:28:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o58_0625/03_2024/6o58_0625.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o58_0625/03_2024/6o58_0625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o58_0625/03_2024/6o58_0625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o58_0625/03_2024/6o58_0625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o58_0625/03_2024/6o58_0625.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o58_0625/03_2024/6o58_0625.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 72 5.16 5 C 13272 2.51 5 N 3526 2.21 5 O 3682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ARG 161": "NH1" <-> "NH2" Residue "O ARG 93": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 124": "NH1" <-> "NH2" Residue "O ARG 134": "NH1" <-> "NH2" Residue "O ARG 295": "NH1" <-> "NH2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ARG 124": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 295": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "I PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 124": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20554 Number of models: 1 Model: "" Number of chains: 18 Chain: "K" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "L" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "O" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "P" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "M" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "N" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "G" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "H" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "I" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "J" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "F" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.20, per 1000 atoms: 0.45 Number of scatterers: 20554 At special positions: 0 Unit cell: (113.4, 215.88, 134.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 72 16.00 O 3682 8.00 N 3526 7.00 C 13272 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: 7.80 Conformation dependent library (CDL) restraints added in 3.2 seconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4816 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 16 sheets defined 64.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'K' and resid 91 through 94 removed outlier: 3.924A pdb=" N ARG K 94 " --> pdb=" O PRO K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 91 through 94' Processing helix chain 'K' and resid 107 through 119 removed outlier: 3.707A pdb=" N LEU K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 Processing helix chain 'K' and resid 172 through 189 removed outlier: 3.620A pdb=" N VAL K 179 " --> pdb=" O THR K 175 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 215 removed outlier: 3.699A pdb=" N GLU K 208 " --> pdb=" O ILE K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 257 removed outlier: 3.627A pdb=" N ARG K 221 " --> pdb=" O LEU K 217 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU K 234 " --> pdb=" O LYS K 230 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL K 235 " --> pdb=" O ARG K 231 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU K 240 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY K 248 " --> pdb=" O ALA K 244 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU K 250 " --> pdb=" O GLN K 246 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG K 252 " --> pdb=" O GLY K 248 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU K 253 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP K 255 " --> pdb=" O ALA K 251 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 286 removed outlier: 3.586A pdb=" N MET K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Proline residue: K 265 - end of helix removed outlier: 3.566A pdb=" N PHE K 269 " --> pdb=" O PRO K 265 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA K 275 " --> pdb=" O THR K 271 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE K 282 " --> pdb=" O MET K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 310 removed outlier: 3.719A pdb=" N ARG K 295 " --> pdb=" O TYR K 291 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP K 296 " --> pdb=" O PRO K 292 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG K 297 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS K 308 " --> pdb=" O HIS K 304 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 309 " --> pdb=" O LYS K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 335 removed outlier: 3.534A pdb=" N GLN K 319 " --> pdb=" O GLU K 315 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP K 322 " --> pdb=" O ASN K 318 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA K 323 " --> pdb=" O GLN K 319 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE K 324 " --> pdb=" O LEU K 320 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA K 325 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG K 335 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 94 Proline residue: L 76 - end of helix removed outlier: 3.985A pdb=" N SER L 85 " --> pdb=" O GLY L 81 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN L 87 " --> pdb=" O LEU L 83 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE L 88 " --> pdb=" O ILE L 84 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 119 removed outlier: 3.993A pdb=" N ARG O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU O 118 " --> pdb=" O GLN O 114 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 188 Processing helix chain 'O' and resid 188 through 256 removed outlier: 3.698A pdb=" N ILE O 192 " --> pdb=" O THR O 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU O 193 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN O 194 " --> pdb=" O LEU O 190 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU O 197 " --> pdb=" O GLU O 193 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU O 202 " --> pdb=" O ASN O 198 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU O 205 " --> pdb=" O ARG O 201 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN O 213 " --> pdb=" O ASP O 209 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA O 215 " --> pdb=" O LYS O 211 " (cutoff:3.500A) Proline residue: O 216 - end of helix removed outlier: 3.691A pdb=" N GLU O 223 " --> pdb=" O LYS O 219 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG O 231 " --> pdb=" O LYS O 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU O 240 " --> pdb=" O LEU O 236 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU O 253 " --> pdb=" O ILE O 249 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR O 254 " --> pdb=" O LEU O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 286 Proline residue: O 265 - end of helix removed outlier: 3.888A pdb=" N PHE O 269 " --> pdb=" O PRO O 265 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE O 270 " --> pdb=" O VAL O 266 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 309 removed outlier: 3.876A pdb=" N ASP O 296 " --> pdb=" O PRO O 292 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU O 300 " --> pdb=" O ASP O 296 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU O 301 " --> pdb=" O ARG O 297 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS O 305 " --> pdb=" O LEU O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 313 through 336 removed outlier: 3.570A pdb=" N TYR O 317 " --> pdb=" O ASP O 313 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN O 319 " --> pdb=" O GLU O 315 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG O 333 " --> pdb=" O MET O 329 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG O 335 " --> pdb=" O LEU O 331 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP O 336 " --> pdb=" O LYS O 332 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 95 removed outlier: 3.514A pdb=" N ARG P 69 " --> pdb=" O PHE P 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER P 72 " --> pdb=" O LEU P 68 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE P 75 " --> pdb=" O PHE P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.609A pdb=" N THR P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU P 91 " --> pdb=" O ASN P 87 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU P 92 " --> pdb=" O PHE P 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 119 removed outlier: 3.586A pdb=" N ARG M 113 " --> pdb=" O GLY M 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 144 Processing helix chain 'M' and resid 169 through 190 removed outlier: 3.510A pdb=" N ALA M 173 " --> pdb=" O SER M 169 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA M 174 " --> pdb=" O HIS M 170 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR M 175 " --> pdb=" O GLU M 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 246 removed outlier: 3.612A pdb=" N LYS M 199 " --> pdb=" O HIS M 195 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU M 200 " --> pdb=" O GLN M 196 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU M 208 " --> pdb=" O ILE M 204 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN M 213 " --> pdb=" O ASP M 209 " (cutoff:3.500A) Proline residue: M 216 - end of helix removed outlier: 3.721A pdb=" N LYS M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS M 227 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL M 235 " --> pdb=" O ARG M 231 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA M 241 " --> pdb=" O TRP M 237 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN M 246 " --> pdb=" O TYR M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 254 removed outlier: 4.013A pdb=" N LEU M 250 " --> pdb=" O GLN M 246 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA M 251 " --> pdb=" O PHE M 247 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 285 removed outlier: 4.060A pdb=" N THR M 267 " --> pdb=" O MET M 263 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA M 275 " --> pdb=" O THR M 271 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET M 276 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE M 282 " --> pdb=" O MET M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 310 removed outlier: 3.583A pdb=" N ARG M 297 " --> pdb=" O GLU M 293 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU M 300 " --> pdb=" O ASP M 296 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS M 304 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS M 305 " --> pdb=" O LEU M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 333 removed outlier: 3.772A pdb=" N LYS M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 96 Proline residue: N 76 - end of helix removed outlier: 3.754A pdb=" N TYR N 79 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL N 80 " --> pdb=" O PRO N 76 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY N 81 " --> pdb=" O PHE N 77 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS N 95 " --> pdb=" O LEU N 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 117 removed outlier: 3.994A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 removed outlier: 3.501A pdb=" N LEU G 144 " --> pdb=" O GLY G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 188 Processing helix chain 'G' and resid 188 through 256 removed outlier: 3.697A pdb=" N ILE G 192 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU G 193 " --> pdb=" O THR G 189 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU G 210 " --> pdb=" O ARG G 206 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 3.689A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE G 247 " --> pdb=" O MET G 243 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU G 253 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 286 Proline residue: G 265 - end of helix removed outlier: 3.822A pdb=" N PHE G 269 " --> pdb=" O PRO G 265 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 270 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE G 282 " --> pdb=" O MET G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 309 removed outlier: 3.897A pdb=" N ASP G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU G 300 " --> pdb=" O ASP G 296 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 336 removed outlier: 3.570A pdb=" N TYR G 317 " --> pdb=" O ASP G 313 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN G 319 " --> pdb=" O GLU G 315 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG G 333 " --> pdb=" O MET G 329 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU G 334 " --> pdb=" O ASP G 330 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP G 336 " --> pdb=" O LYS G 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 95 removed outlier: 3.508A pdb=" N ARG H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Proline residue: H 76 - end of helix removed outlier: 3.863A pdb=" N SER H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 92 " --> pdb=" O PHE H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 119 removed outlier: 4.122A pdb=" N ARG I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 145 Processing helix chain 'I' and resid 172 through 191 removed outlier: 3.721A pdb=" N ASP I 178 " --> pdb=" O ALA I 174 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 213 removed outlier: 3.866A pdb=" N HIS I 195 " --> pdb=" O CYS I 191 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU I 202 " --> pdb=" O ASN I 198 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU I 208 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 210 " --> pdb=" O ARG I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 250 removed outlier: 4.223A pdb=" N LEU I 217 " --> pdb=" O GLN I 213 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS I 219 " --> pdb=" O ALA I 215 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU I 234 " --> pdb=" O LYS I 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN I 246 " --> pdb=" O TYR I 242 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE I 247 " --> pdb=" O MET I 243 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU I 250 " --> pdb=" O GLN I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 259 through 285 removed outlier: 3.565A pdb=" N MET I 263 " --> pdb=" O SER I 259 " (cutoff:3.500A) Proline residue: I 265 - end of helix removed outlier: 3.811A pdb=" N THR I 271 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET I 276 " --> pdb=" O TYR I 272 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR I 281 " --> pdb=" O ALA I 277 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE I 282 " --> pdb=" O MET I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 293 Processing helix chain 'I' and resid 294 through 310 removed outlier: 3.985A pdb=" N LEU I 300 " --> pdb=" O ASP I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 340 removed outlier: 3.994A pdb=" N TYR I 317 " --> pdb=" O ASP I 313 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN I 319 " --> pdb=" O GLU I 315 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE I 324 " --> pdb=" O LEU I 320 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP I 336 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Proline residue: I 337 - end of helix Processing helix chain 'J' and resid 67 through 75 removed outlier: 3.596A pdb=" N ILE J 75 " --> pdb=" O PHE J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 96 removed outlier: 3.764A pdb=" N TYR J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU J 91 " --> pdb=" O ASN J 87 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 94 removed outlier: 3.699A pdb=" N ARG C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 91 through 94' Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.686A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 172 through 189 removed outlier: 3.628A pdb=" N VAL C 179 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.693A pdb=" N GLU C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 257 removed outlier: 3.628A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 removed outlier: 3.592A pdb=" N MET C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 3.553A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 310 removed outlier: 3.717A pdb=" N ARG C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.533A pdb=" N GLN C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 94 Proline residue: D 76 - end of helix removed outlier: 3.953A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 119 removed outlier: 4.109A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.718A pdb=" N ASP A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 213 removed outlier: 3.777A pdb=" N HIS A 195 " --> pdb=" O CYS A 191 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 250 removed outlier: 4.372A pdb=" N LEU A 217 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.784A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 310 removed outlier: 3.800A pdb=" N ARG A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 334 removed outlier: 3.992A pdb=" N TYR A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.901A pdb=" N LEU A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 75 through 96 removed outlier: 3.735A pdb=" N TYR B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.620A pdb=" N ARG E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 169 through 190 removed outlier: 3.593A pdb=" N ALA E 174 " --> pdb=" O HIS E 170 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 246 removed outlier: 3.643A pdb=" N LYS E 199 " --> pdb=" O HIS E 195 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU E 208 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.659A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS E 227 " --> pdb=" O GLU E 223 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN E 246 " --> pdb=" O TYR E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 254 removed outlier: 4.044A pdb=" N LEU E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 285 removed outlier: 3.613A pdb=" N THR E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 270 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 310 removed outlier: 3.583A pdb=" N ARG E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 300 " --> pdb=" O ASP E 296 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 333 removed outlier: 3.726A pdb=" N LYS E 321 " --> pdb=" O TYR E 317 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 96 Proline residue: F 76 - end of helix removed outlier: 3.756A pdb=" N TYR F 79 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL F 80 " --> pdb=" O PRO F 76 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 81 " --> pdb=" O PHE F 77 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AA2, first strand: chain 'K' and resid 126 through 128 removed outlier: 3.585A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 134 through 135 removed outlier: 3.796A pdb=" N THR I 76 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 77 through 78 removed outlier: 3.614A pdb=" N VAL O 78 " --> pdb=" O VAL O 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 125 through 128 removed outlier: 3.588A pdb=" N PHE O 149 " --> pdb=" O VAL O 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 134 through 135 removed outlier: 6.982A pdb=" N ARG O 134 " --> pdb=" O GLN M 98 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N THR M 100 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR M 76 " --> pdb=" O SER M 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 126 through 127 Processing sheet with id=AA8, first strand: chain 'G' and resid 76 through 78 removed outlier: 4.634A pdb=" N THR G 76 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER G 87 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 78 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 125 through 128 removed outlier: 3.597A pdb=" N PHE G 149 " --> pdb=" O VAL G 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 134 through 135 removed outlier: 6.982A pdb=" N ARG G 134 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR E 100 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 76 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 80 Processing sheet with id=AB4, first strand: chain 'C' and resid 126 through 128 Processing sheet with id=AB5, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.844A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AB7, first strand: chain 'E' and resid 126 through 127 1106 hydrogen bonds defined for protein. 3207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 8.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6551 1.34 - 1.46: 4567 1.46 - 1.58: 9726 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 20972 Sorted by residual: bond pdb=" C ILE J 75 " pdb=" N PRO J 76 " ideal model delta sigma weight residual 1.336 1.400 -0.064 1.20e-02 6.94e+03 2.85e+01 bond pdb=" N GLU A 257 " pdb=" CA GLU A 257 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.09e-02 8.42e+03 1.12e+01 bond pdb=" C ALA M 215 " pdb=" N PRO M 216 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.20e-02 6.94e+03 9.44e+00 bond pdb=" N GLU M 257 " pdb=" CA GLU M 257 " ideal model delta sigma weight residual 1.455 1.496 -0.042 1.37e-02 5.33e+03 9.33e+00 bond pdb=" N GLU E 257 " pdb=" CA GLU E 257 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.37e-02 5.33e+03 9.08e+00 ... (remaining 20967 not shown) Histogram of bond angle deviations from ideal: 98.06 - 106.02: 469 106.02 - 113.98: 11882 113.98 - 121.95: 11973 121.95 - 129.91: 3919 129.91 - 137.87: 145 Bond angle restraints: 28388 Sorted by residual: angle pdb=" C ARG C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta sigma weight residual 120.38 112.08 8.30 1.03e+00 9.43e-01 6.49e+01 angle pdb=" CA TYR A 258 " pdb=" C TYR A 258 " pdb=" O TYR A 258 " ideal model delta sigma weight residual 120.51 111.83 8.68 1.43e+00 4.89e-01 3.69e+01 angle pdb=" N PRO K 162 " pdb=" CA PRO K 162 " pdb=" C PRO K 162 " ideal model delta sigma weight residual 110.70 117.89 -7.19 1.22e+00 6.72e-01 3.47e+01 angle pdb=" C ILE E 153 " pdb=" N ASN E 154 " pdb=" CA ASN E 154 " ideal model delta sigma weight residual 121.19 130.43 -9.24 1.59e+00 3.96e-01 3.37e+01 angle pdb=" CA PRO K 162 " pdb=" C PRO K 162 " pdb=" N PRO K 163 " ideal model delta sigma weight residual 117.93 124.63 -6.70 1.20e+00 6.94e-01 3.11e+01 ... (remaining 28383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 11810 15.31 - 30.63: 685 30.63 - 45.94: 229 45.94 - 61.25: 11 61.25 - 76.57: 21 Dihedral angle restraints: 12756 sinusoidal: 5326 harmonic: 7430 Sorted by residual: dihedral pdb=" CA ARG K 161 " pdb=" C ARG K 161 " pdb=" N PRO K 162 " pdb=" CA PRO K 162 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE E 153 " pdb=" C ILE E 153 " pdb=" N ASN E 154 " pdb=" CA ASN E 154 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ILE K 153 " pdb=" C ILE K 153 " pdb=" N ASN K 154 " pdb=" CA ASN K 154 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 12753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2480 0.064 - 0.128: 639 0.128 - 0.192: 94 0.192 - 0.256: 16 0.256 - 0.321: 5 Chirality restraints: 3234 Sorted by residual: chirality pdb=" CB ILE K 86 " pdb=" CA ILE K 86 " pdb=" CG1 ILE K 86 " pdb=" CG2 ILE K 86 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE M 122 " pdb=" CA ILE M 122 " pdb=" CG1 ILE M 122 " pdb=" CG2 ILE M 122 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE E 122 " pdb=" CA ILE E 122 " pdb=" CG1 ILE E 122 " pdb=" CG2 ILE E 122 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 3231 not shown) Planarity restraints: 3578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 161 " 0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO K 162 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO K 162 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 162 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 258 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C TYR A 258 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR A 258 " 0.021 2.00e-02 2.50e+03 pdb=" N SER A 259 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 256 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C TRP E 256 " -0.050 2.00e-02 2.50e+03 pdb=" O TRP E 256 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU E 257 " 0.017 2.00e-02 2.50e+03 ... (remaining 3575 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4955 2.80 - 3.32: 18351 3.32 - 3.85: 32305 3.85 - 4.37: 35037 4.37 - 4.90: 60006 Nonbonded interactions: 150654 Sorted by model distance: nonbonded pdb=" OG SER A 259 " pdb=" N TRP A 260 " model vdw 2.271 2.520 nonbonded pdb=" O GLN E 185 " pdb=" OG1 THR E 189 " model vdw 2.282 2.440 nonbonded pdb=" O GLN M 185 " pdb=" OG1 THR M 189 " model vdw 2.285 2.440 nonbonded pdb=" OG SER E 225 " pdb=" OH TYR E 299 " model vdw 2.289 2.440 nonbonded pdb=" OE1 GLU E 218 " pdb=" OH TYR E 317 " model vdw 2.297 2.440 ... (remaining 150649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'C' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'E' and (resid 75 through 164 or resid 177 through 336)) selection = chain 'G' selection = (chain 'I' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'K' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'M' and (resid 75 through 164 or resid 177 through 336)) selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 48 through 95) selection = (chain 'D' and resid 48 through 95) selection = (chain 'F' and resid 48 through 95) selection = chain 'H' selection = (chain 'J' and resid 48 through 95) selection = (chain 'L' and resid 48 through 95) selection = (chain 'N' and resid 48 through 95) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.630 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 47.940 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.005 0.077 20972 Z= 0.326 Angle : 1.074 12.875 28388 Z= 0.571 Chirality : 0.058 0.321 3234 Planarity : 0.007 0.102 3578 Dihedral : 11.586 76.565 7940 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 0.31 % Allowed : 7.17 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.97 (0.13), residues: 2476 helix: -2.63 (0.09), residues: 1498 sheet: -1.49 (0.34), residues: 196 loop : -2.49 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 260 HIS 0.009 0.001 HIS E 341 PHE 0.024 0.002 PHE C 312 TYR 0.023 0.002 TYR O 79 ARG 0.007 0.001 ARG K 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 394 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.8299 (ttm) cc_final: 0.8063 (tpp) REVERT: K 329 MET cc_start: 0.8833 (tmm) cc_final: 0.8473 (tmm) REVERT: O 311 ARG cc_start: 0.6625 (mpt-90) cc_final: 0.6346 (ttp80) REVERT: O 316 LYS cc_start: 0.8452 (mtpm) cc_final: 0.7808 (tppt) REVERT: P 84 ILE cc_start: 0.7203 (pp) cc_final: 0.6735 (mm) REVERT: M 284 MET cc_start: 0.7910 (mtt) cc_final: 0.7668 (mtm) REVERT: G 263 MET cc_start: 0.7390 (ttt) cc_final: 0.7158 (tpt) REVERT: G 311 ARG cc_start: 0.6629 (mpt-90) cc_final: 0.6345 (ttp80) REVERT: G 316 LYS cc_start: 0.8464 (mtpm) cc_final: 0.7821 (tppt) REVERT: I 243 MET cc_start: 0.7349 (ttm) cc_final: 0.6806 (mtt) REVERT: C 276 MET cc_start: 0.8352 (ttm) cc_final: 0.8107 (tpp) REVERT: C 329 MET cc_start: 0.8804 (tmm) cc_final: 0.8442 (tmm) REVERT: A 243 MET cc_start: 0.7408 (ttm) cc_final: 0.6844 (mtt) REVERT: B 70 VAL cc_start: 0.8841 (t) cc_final: 0.8535 (p) REVERT: E 284 MET cc_start: 0.7912 (mtt) cc_final: 0.7668 (mtm) outliers start: 7 outliers final: 2 residues processed: 401 average time/residue: 0.3976 time to fit residues: 225.9487 Evaluate side-chains 166 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 258 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 219 optimal weight: 0.5980 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 114 GLN K 177 ASN K 194 GLN K 304 HIS O 196 GLN M 184 GLN N 87 ASN G 196 GLN I 80 GLN I 177 ASN C 114 GLN C 159 HIS C 177 ASN C 194 GLN C 246 GLN C 304 HIS A 80 GLN A 177 ASN E 184 GLN E 339 GLN F 87 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20972 Z= 0.260 Angle : 0.678 9.281 28388 Z= 0.347 Chirality : 0.043 0.145 3234 Planarity : 0.006 0.103 3578 Dihedral : 5.540 59.877 2811 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 3.12 % Allowed : 12.92 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2476 helix: -0.74 (0.12), residues: 1510 sheet: -0.78 (0.34), residues: 216 loop : -1.97 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 260 HIS 0.007 0.001 HIS K 159 PHE 0.022 0.002 PHE M 312 TYR 0.023 0.002 TYR C 268 ARG 0.012 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 163 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 329 MET cc_start: 0.8755 (tmm) cc_final: 0.8531 (tmm) REVERT: O 311 ARG cc_start: 0.6630 (mpt-90) cc_final: 0.6249 (ttp80) REVERT: O 316 LYS cc_start: 0.8428 (mtpm) cc_final: 0.7780 (tppt) REVERT: P 51 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7991 (p) REVERT: G 311 ARG cc_start: 0.6623 (mpt-90) cc_final: 0.6248 (ttp80) REVERT: G 316 LYS cc_start: 0.8443 (mtpm) cc_final: 0.7793 (tppt) REVERT: J 69 ARG cc_start: 0.6624 (ptt180) cc_final: 0.6282 (tpt170) REVERT: C 276 MET cc_start: 0.8467 (ttm) cc_final: 0.8177 (tpp) REVERT: C 329 MET cc_start: 0.8736 (tmm) cc_final: 0.8518 (tmm) REVERT: B 70 VAL cc_start: 0.8711 (t) cc_final: 0.8414 (p) outliers start: 70 outliers final: 25 residues processed: 223 average time/residue: 0.2884 time to fit residues: 104.8243 Evaluate side-chains 157 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 249 ILE Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 77 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 194 GLN N 95 HIS C 194 GLN F 95 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 20972 Z= 0.293 Angle : 0.672 8.630 28388 Z= 0.341 Chirality : 0.043 0.169 3234 Planarity : 0.005 0.097 3578 Dihedral : 5.223 29.107 2806 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.52 % Allowed : 14.88 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2476 helix: -0.05 (0.13), residues: 1516 sheet: -0.69 (0.38), residues: 196 loop : -1.69 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.011 0.001 HIS K 159 PHE 0.022 0.002 PHE M 312 TYR 0.029 0.002 TYR K 268 ARG 0.004 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 130 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.8413 (tpp) cc_final: 0.7605 (tpt) REVERT: O 311 ARG cc_start: 0.6706 (mpt-90) cc_final: 0.6291 (ttp80) REVERT: O 316 LYS cc_start: 0.8559 (mtpm) cc_final: 0.7760 (tppt) REVERT: P 51 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7985 (p) REVERT: G 311 ARG cc_start: 0.6700 (mpt-90) cc_final: 0.6283 (ttp80) REVERT: G 316 LYS cc_start: 0.8572 (mtpm) cc_final: 0.7777 (tppt) REVERT: I 243 MET cc_start: 0.7453 (ttt) cc_final: 0.6163 (ttt) REVERT: J 69 ARG cc_start: 0.6809 (ptt180) cc_final: 0.6338 (tpt170) REVERT: C 243 MET cc_start: 0.8552 (mtm) cc_final: 0.7918 (ptp) REVERT: C 276 MET cc_start: 0.8527 (ttm) cc_final: 0.8238 (tpp) REVERT: A 145 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8593 (mm) REVERT: B 70 VAL cc_start: 0.8716 (t) cc_final: 0.8393 (p) outliers start: 79 outliers final: 37 residues processed: 201 average time/residue: 0.2862 time to fit residues: 94.4406 Evaluate side-chains 160 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 HIS K 194 GLN ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 HIS E 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 20972 Z= 0.297 Angle : 0.665 8.630 28388 Z= 0.337 Chirality : 0.043 0.190 3234 Planarity : 0.005 0.089 3578 Dihedral : 5.090 28.277 2806 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.43 % Allowed : 16.44 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2476 helix: 0.29 (0.13), residues: 1526 sheet: -0.64 (0.38), residues: 196 loop : -1.68 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 256 HIS 0.009 0.001 HIS K 159 PHE 0.021 0.002 PHE M 312 TYR 0.021 0.002 TYR K 268 ARG 0.004 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 118 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.8459 (tpp) cc_final: 0.7523 (tpt) REVERT: L 49 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.7014 (pt) REVERT: O 177 ASN cc_start: 0.6547 (OUTLIER) cc_final: 0.6329 (t0) REVERT: O 311 ARG cc_start: 0.6716 (mpt-90) cc_final: 0.6283 (ttp80) REVERT: P 51 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (p) REVERT: M 329 MET cc_start: 0.8676 (tpp) cc_final: 0.8455 (tpp) REVERT: G 177 ASN cc_start: 0.6478 (OUTLIER) cc_final: 0.6263 (t0) REVERT: G 311 ARG cc_start: 0.6706 (mpt-90) cc_final: 0.6272 (ttp80) REVERT: I 243 MET cc_start: 0.7420 (ttt) cc_final: 0.6111 (ttt) REVERT: C 243 MET cc_start: 0.8636 (mtm) cc_final: 0.7941 (ptp) REVERT: C 276 MET cc_start: 0.8525 (ttm) cc_final: 0.8218 (tpp) REVERT: D 49 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.7005 (pt) REVERT: B 70 VAL cc_start: 0.8849 (t) cc_final: 0.8526 (p) REVERT: E 300 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8742 (tt) REVERT: E 329 MET cc_start: 0.8615 (tpp) cc_final: 0.8347 (tpp) outliers start: 77 outliers final: 47 residues processed: 182 average time/residue: 0.2636 time to fit residues: 80.7210 Evaluate side-chains 164 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 111 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 177 ASN Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 174 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 194 GLN ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 20972 Z= 0.321 Angle : 0.676 8.759 28388 Z= 0.342 Chirality : 0.043 0.159 3234 Planarity : 0.005 0.089 3578 Dihedral : 5.108 28.693 2806 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.06 % Allowed : 17.56 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2476 helix: 0.41 (0.13), residues: 1528 sheet: -0.61 (0.39), residues: 196 loop : -1.69 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 256 HIS 0.023 0.002 HIS K 159 PHE 0.020 0.002 PHE M 312 TYR 0.016 0.002 TYR O 317 ARG 0.003 0.001 ARG M 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 110 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 243 MET cc_start: 0.8762 (ptm) cc_final: 0.8135 (ptm) REVERT: K 276 MET cc_start: 0.8490 (tpp) cc_final: 0.7602 (tpt) REVERT: O 311 ARG cc_start: 0.6782 (mpt-90) cc_final: 0.6327 (ttp80) REVERT: P 51 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8034 (p) REVERT: G 276 MET cc_start: 0.7880 (tpp) cc_final: 0.7525 (tpp) REVERT: G 311 ARG cc_start: 0.6813 (mpt-90) cc_final: 0.6319 (ttp80) REVERT: I 243 MET cc_start: 0.7411 (ttt) cc_final: 0.6047 (ttt) REVERT: C 243 MET cc_start: 0.8660 (mtm) cc_final: 0.7697 (ptp) REVERT: C 276 MET cc_start: 0.8504 (ttm) cc_final: 0.8212 (tpp) REVERT: B 70 VAL cc_start: 0.8916 (t) cc_final: 0.8582 (p) outliers start: 91 outliers final: 58 residues processed: 191 average time/residue: 0.2782 time to fit residues: 86.4533 Evaluate side-chains 168 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 109 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 138 SER Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 HIS L 95 HIS ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 20972 Z= 0.294 Angle : 0.664 13.533 28388 Z= 0.332 Chirality : 0.043 0.154 3234 Planarity : 0.005 0.088 3578 Dihedral : 4.990 28.293 2806 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.74 % Allowed : 18.58 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2476 helix: 0.53 (0.13), residues: 1526 sheet: -0.51 (0.40), residues: 196 loop : -1.64 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 256 HIS 0.005 0.001 HIS M 170 PHE 0.020 0.002 PHE M 312 TYR 0.016 0.002 TYR O 317 ARG 0.004 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 112 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 243 MET cc_start: 0.8721 (ptm) cc_final: 0.8143 (ptm) REVERT: K 276 MET cc_start: 0.8508 (tpp) cc_final: 0.7715 (tpt) REVERT: O 311 ARG cc_start: 0.6873 (mpt-90) cc_final: 0.6333 (ttp80) REVERT: O 329 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6516 (tpt) REVERT: P 51 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8032 (p) REVERT: M 329 MET cc_start: 0.8690 (tpp) cc_final: 0.8359 (tpp) REVERT: G 276 MET cc_start: 0.7873 (tpp) cc_final: 0.7520 (tpp) REVERT: G 311 ARG cc_start: 0.6869 (mpt-90) cc_final: 0.6322 (ttp80) REVERT: I 243 MET cc_start: 0.7406 (ttt) cc_final: 0.6050 (ttt) REVERT: C 243 MET cc_start: 0.8648 (mtm) cc_final: 0.7691 (ptp) REVERT: C 276 MET cc_start: 0.8521 (ttm) cc_final: 0.8046 (tpt) REVERT: B 70 VAL cc_start: 0.8886 (t) cc_final: 0.8586 (p) outliers start: 84 outliers final: 56 residues processed: 185 average time/residue: 0.2608 time to fit residues: 80.6510 Evaluate side-chains 166 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 108 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 191 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 138 SER Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 77 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 107 optimal weight: 0.0980 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 HIS A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20972 Z= 0.176 Angle : 0.599 14.039 28388 Z= 0.294 Chirality : 0.041 0.151 3234 Planarity : 0.004 0.088 3578 Dihedral : 4.696 28.619 2806 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.72 % Allowed : 19.61 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2476 helix: 0.90 (0.14), residues: 1524 sheet: -0.33 (0.40), residues: 196 loop : -1.45 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 256 HIS 0.027 0.001 HIS K 159 PHE 0.021 0.001 PHE M 312 TYR 0.018 0.001 TYR K 158 ARG 0.007 0.000 ARG K 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 122 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.8497 (tpp) cc_final: 0.7672 (tpt) REVERT: O 90 LEU cc_start: 0.4621 (OUTLIER) cc_final: 0.3985 (tp) REVERT: O 150 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7745 (ptpp) REVERT: O 234 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9080 (tt) REVERT: O 311 ARG cc_start: 0.6804 (mpt-90) cc_final: 0.6326 (ttp80) REVERT: O 329 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6418 (tpt) REVERT: P 51 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7922 (t) REVERT: M 329 MET cc_start: 0.8631 (tpp) cc_final: 0.8387 (tpp) REVERT: G 234 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9084 (tt) REVERT: G 311 ARG cc_start: 0.6788 (mpt-90) cc_final: 0.6304 (ttp80) REVERT: I 243 MET cc_start: 0.7305 (ttt) cc_final: 0.6177 (ttt) REVERT: C 276 MET cc_start: 0.8556 (ttm) cc_final: 0.8232 (tpp) REVERT: C 284 MET cc_start: 0.7017 (ttm) cc_final: 0.6815 (tmm) REVERT: B 70 VAL cc_start: 0.8968 (t) cc_final: 0.8677 (p) REVERT: E 329 MET cc_start: 0.8670 (tpp) cc_final: 0.8388 (tpp) outliers start: 61 outliers final: 37 residues processed: 178 average time/residue: 0.2664 time to fit residues: 78.4435 Evaluate side-chains 154 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 191 CYS Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 77 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 183 optimal weight: 0.4980 chunk 212 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20972 Z= 0.182 Angle : 0.602 13.998 28388 Z= 0.294 Chirality : 0.041 0.161 3234 Planarity : 0.004 0.089 3578 Dihedral : 4.564 28.978 2806 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.76 % Allowed : 20.14 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 2476 helix: 1.05 (0.14), residues: 1524 sheet: -0.23 (0.41), residues: 196 loop : -1.33 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 256 HIS 0.014 0.001 HIS K 159 PHE 0.020 0.001 PHE M 312 TYR 0.016 0.001 TYR K 158 ARG 0.004 0.000 ARG K 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 113 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.8513 (tpp) cc_final: 0.7644 (tpt) REVERT: O 90 LEU cc_start: 0.4471 (OUTLIER) cc_final: 0.3867 (tp) REVERT: O 150 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7665 (ptpt) REVERT: O 311 ARG cc_start: 0.6792 (mpt-90) cc_final: 0.6318 (ttp80) REVERT: O 329 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.6349 (tpt) REVERT: P 51 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7940 (p) REVERT: M 329 MET cc_start: 0.8643 (tpp) cc_final: 0.8413 (tpp) REVERT: G 90 LEU cc_start: 0.4455 (OUTLIER) cc_final: 0.3836 (tp) REVERT: G 234 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9080 (tt) REVERT: G 311 ARG cc_start: 0.6792 (mpt-90) cc_final: 0.6310 (ttp80) REVERT: I 243 MET cc_start: 0.7255 (ttt) cc_final: 0.6055 (ttt) REVERT: C 243 MET cc_start: 0.8414 (mtm) cc_final: 0.7773 (ptp) REVERT: C 284 MET cc_start: 0.7032 (ttm) cc_final: 0.6786 (tmm) REVERT: A 276 MET cc_start: 0.7922 (mmm) cc_final: 0.7648 (mmt) REVERT: B 70 VAL cc_start: 0.8996 (t) cc_final: 0.8705 (p) REVERT: E 329 MET cc_start: 0.8659 (tpp) cc_final: 0.8402 (tpp) outliers start: 62 outliers final: 37 residues processed: 173 average time/residue: 0.2653 time to fit residues: 76.2350 Evaluate side-chains 151 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 108 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 159 HIS Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 191 CYS Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 HIS ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 20972 Z= 0.353 Angle : 0.694 12.685 28388 Z= 0.348 Chirality : 0.043 0.147 3234 Planarity : 0.005 0.088 3578 Dihedral : 4.892 28.317 2806 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.94 % Allowed : 20.28 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2476 helix: 0.73 (0.13), residues: 1526 sheet: -0.36 (0.40), residues: 196 loop : -1.48 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 256 HIS 0.025 0.002 HIS K 159 PHE 0.020 0.002 PHE M 312 TYR 0.015 0.002 TYR J 79 ARG 0.004 0.001 ARG K 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 105 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.8508 (tpp) cc_final: 0.7838 (tpt) REVERT: K 284 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6480 (tmm) REVERT: O 150 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7625 (ptpt) REVERT: O 234 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9082 (tt) REVERT: O 311 ARG cc_start: 0.6893 (mpt-90) cc_final: 0.6323 (ttp80) REVERT: O 329 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6501 (tpt) REVERT: P 51 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8017 (p) REVERT: M 329 MET cc_start: 0.8728 (tpp) cc_final: 0.8446 (tpp) REVERT: G 99 PHE cc_start: 0.7070 (m-80) cc_final: 0.6830 (m-80) REVERT: G 258 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: G 311 ARG cc_start: 0.6898 (mpt-90) cc_final: 0.6316 (ttp80) REVERT: I 243 MET cc_start: 0.7485 (ttt) cc_final: 0.6124 (ttt) REVERT: C 276 MET cc_start: 0.8548 (ttm) cc_final: 0.8230 (tpp) REVERT: A 276 MET cc_start: 0.7976 (mmm) cc_final: 0.7734 (mmt) REVERT: B 70 VAL cc_start: 0.8959 (t) cc_final: 0.8681 (p) outliers start: 66 outliers final: 48 residues processed: 163 average time/residue: 0.2571 time to fit residues: 70.5896 Evaluate side-chains 157 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 103 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 284 MET Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 263 MET Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 191 CYS Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 241 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20972 Z= 0.253 Angle : 0.643 13.626 28388 Z= 0.316 Chirality : 0.042 0.137 3234 Planarity : 0.004 0.085 3578 Dihedral : 4.779 28.844 2806 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.63 % Allowed : 20.72 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2476 helix: 0.86 (0.14), residues: 1524 sheet: -0.27 (0.40), residues: 202 loop : -1.42 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 256 HIS 0.006 0.001 HIS K 159 PHE 0.020 0.002 PHE M 312 TYR 0.013 0.001 TYR O 317 ARG 0.006 0.000 ARG K 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 109 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 243 MET cc_start: 0.8442 (ptp) cc_final: 0.8132 (ptm) REVERT: K 276 MET cc_start: 0.8490 (tpp) cc_final: 0.7759 (tpt) REVERT: O 150 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7685 (ptpt) REVERT: O 234 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9078 (tt) REVERT: O 311 ARG cc_start: 0.6913 (mpt-90) cc_final: 0.6356 (ttp80) REVERT: O 329 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6501 (tpt) REVERT: P 51 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7983 (p) REVERT: M 329 MET cc_start: 0.8686 (tpp) cc_final: 0.8407 (tpp) REVERT: G 99 PHE cc_start: 0.6999 (m-80) cc_final: 0.6751 (m-80) REVERT: G 234 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9076 (tt) REVERT: G 258 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8364 (m-10) REVERT: G 311 ARG cc_start: 0.6911 (mpt-90) cc_final: 0.6350 (ttp80) REVERT: I 243 MET cc_start: 0.7423 (ttt) cc_final: 0.6145 (ttt) REVERT: C 243 MET cc_start: 0.8394 (mtm) cc_final: 0.7909 (ptm) REVERT: C 276 MET cc_start: 0.8563 (ttm) cc_final: 0.8227 (tpp) REVERT: B 70 VAL cc_start: 0.8983 (t) cc_final: 0.8710 (p) REVERT: E 329 MET cc_start: 0.8695 (tpp) cc_final: 0.8396 (tpp) outliers start: 59 outliers final: 49 residues processed: 163 average time/residue: 0.2631 time to fit residues: 72.7218 Evaluate side-chains 159 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 104 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain O residue 81 ASN Chi-restraints excluded: chain O residue 150 LYS Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 290 VAL Chi-restraints excluded: chain O residue 329 MET Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 172 ASN Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 191 CYS Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.071029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062784 restraints weight = 113160.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063430 restraints weight = 60272.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.063744 restraints weight = 43167.934| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 20972 Z= 0.376 Angle : 0.720 12.720 28388 Z= 0.360 Chirality : 0.044 0.144 3234 Planarity : 0.005 0.085 3578 Dihedral : 5.046 28.706 2806 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.85 % Allowed : 20.68 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2476 helix: 0.58 (0.13), residues: 1526 sheet: -0.40 (0.39), residues: 202 loop : -1.55 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 256 HIS 0.006 0.001 HIS M 170 PHE 0.019 0.002 PHE M 312 TYR 0.015 0.002 TYR O 317 ARG 0.005 0.001 ARG K 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.30 seconds wall clock time: 62 minutes 0.62 seconds (3720.62 seconds total)