Starting phenix.real_space_refine on Sun Feb 18 15:42:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgw_10186/02_2024/6sgw_10186.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgw_10186/02_2024/6sgw_10186.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/6sgw_10186/02_2024/6sgw_10186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgw_10186/02_2024/6sgw_10186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgw_10186/02_2024/6sgw_10186.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgw_10186/02_2024/6sgw_10186.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= 0.003 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 14396 2.51 5 N 4020 2.21 5 O 3976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ASP 455": "OD1" <-> "OD2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F ASP 320": "OD1" <-> "OD2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F ARG 366": "NH1" <-> "NH2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ASP 378": "OD1" <-> "OD2" Residue "E TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ASP 437": "OD1" <-> "OD2" Residue "E PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ASP 237": "OD1" <-> "OD2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 406": "NH1" <-> "NH2" Residue "H ASP 437": "OD1" <-> "OD2" Residue "H ASP 455": "OD1" <-> "OD2" Residue "J ARG 10": "NH1" <-> "NH2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J ASP 149": "OD1" <-> "OD2" Residue "J ASP 154": "OD1" <-> "OD2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "J ARG 214": "NH1" <-> "NH2" Residue "J GLU 288": "OE1" <-> "OE2" Residue "J ARG 369": "NH1" <-> "NH2" Residue "G ARG 4": "NH1" <-> "NH2" Residue "G PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G ARG 112": "NH1" <-> "NH2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G ASP 127": "OD1" <-> "OD2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G ARG 242": "NH1" <-> "NH2" Residue "G ARG 264": "NH1" <-> "NH2" Residue "G GLU 276": "OE1" <-> "OE2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22448 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "B" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3055 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 2 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3168 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 27, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2667 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 29, 'TRANS': 306} Chain breaks: 4 Chain: "E" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3055 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 2 Chain: "H" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3168 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 27, 'TRANS': 414} Chain breaks: 3 Chain: "I" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 461 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "J" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2574 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 26, 'TRANS': 297} Chain breaks: 4 Chain: "G" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1829 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 7 Chain: "D" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1829 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 7 Time building chain proxies: 12.06, per 1000 atoms: 0.54 Number of scatterers: 22448 At special positions: 0 Unit cell: (192.494, 144.636, 155.271, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3976 8.00 N 4020 7.00 C 14396 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: 8.98 Conformation dependent library (CDL) restraints added in 4.5 seconds 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5624 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 15 sheets defined 55.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.894A pdb=" N VAL A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.546A pdb=" N THR A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 removed outlier: 4.090A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.601A pdb=" N PHE B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 158 removed outlier: 3.766A pdb=" N HIS B 131 " --> pdb=" O TRP B 127 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 3.507A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.741A pdb=" N GLY B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 234 removed outlier: 3.956A pdb=" N LEU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 263 Processing helix chain 'B' and resid 269 through 285 removed outlier: 4.338A pdb=" N CYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 319 through 349 removed outlier: 4.358A pdb=" N ARG B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.527A pdb=" N TRP B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 364 " --> pdb=" O TRP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.779A pdb=" N LYS B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 430 removed outlier: 4.075A pdb=" N ASN B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 455 removed outlier: 3.797A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.557A pdb=" N VAL B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.862A pdb=" N ILE C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) Proline residue: C 40 - end of helix Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.556A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.804A pdb=" N ALA C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 181 removed outlier: 3.632A pdb=" N VAL C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 198 through 207 removed outlier: 4.143A pdb=" N ALA C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 233 Processing helix chain 'C' and resid 241 through 264 removed outlier: 3.850A pdb=" N THR C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 285 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 313 through 319 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.555A pdb=" N ARG C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 325 " --> pdb=" O PRO C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 4.247A pdb=" N VAL C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 373 Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 379 through 388 Processing helix chain 'C' and resid 388 through 404 Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 440 through 467 removed outlier: 4.090A pdb=" N ASP C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 93 through 130 removed outlier: 3.905A pdb=" N VAL F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 142 removed outlier: 3.896A pdb=" N ALA F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE F 139 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Proline residue: F 140 - end of helix Processing helix chain 'F' and resid 185 through 197 removed outlier: 3.630A pdb=" N ASP F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 239 removed outlier: 3.792A pdb=" N ALA F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 removed outlier: 3.506A pdb=" N TRP F 260 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP F 263 " --> pdb=" O TRP F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 removed outlier: 3.973A pdb=" N ASP F 268 " --> pdb=" O PRO F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 386 through 398 Processing helix chain 'E' and resid 34 through 47 removed outlier: 3.822A pdb=" N ILE E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Proline residue: E 40 - end of helix removed outlier: 3.627A pdb=" N GLN E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.879A pdb=" N VAL E 86 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY E 87 " --> pdb=" O ASP E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 87' Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 127 through 157 removed outlier: 3.641A pdb=" N HIS E 131 " --> pdb=" O TRP E 127 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA E 133 " --> pdb=" O PRO E 129 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 181 removed outlier: 3.959A pdb=" N VAL E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 214 through 233 removed outlier: 4.017A pdb=" N LEU E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 263 Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 285 through 293 removed outlier: 3.875A pdb=" N LEU E 289 " --> pdb=" O GLN E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 350 removed outlier: 3.715A pdb=" N ARG E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG E 325 " --> pdb=" O PRO E 321 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER E 346 " --> pdb=" O GLY E 342 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.519A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL E 364 " --> pdb=" O TRP E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 404 removed outlier: 3.975A pdb=" N LYS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 430 removed outlier: 3.587A pdb=" N ASN E 430 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 removed outlier: 3.759A pdb=" N THR E 438 " --> pdb=" O SER E 435 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR E 439 " --> pdb=" O PRO E 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 439' Processing helix chain 'E' and resid 440 through 456 removed outlier: 4.163A pdb=" N ARG E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 456 " --> pdb=" O THR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'H' and resid 34 through 37 Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.649A pdb=" N VAL H 42 " --> pdb=" O ILE H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 123 removed outlier: 3.717A pdb=" N PHE H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 158 removed outlier: 3.519A pdb=" N ARG H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE H 157 " --> pdb=" O ALA H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 179 removed outlier: 3.737A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H 179 " --> pdb=" O VAL H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 196 Processing helix chain 'H' and resid 198 through 204 Processing helix chain 'H' and resid 215 through 234 removed outlier: 3.576A pdb=" N LEU H 219 " --> pdb=" O PRO H 215 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY H 234 " --> pdb=" O ILE H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 262 removed outlier: 3.833A pdb=" N THR H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA H 260 " --> pdb=" O LEU H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 285 Processing helix chain 'H' and resid 287 through 294 removed outlier: 3.844A pdb=" N ALA H 294 " --> pdb=" O SER H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 345 removed outlier: 3.565A pdb=" N ARG H 323 " --> pdb=" O ASP H 319 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG H 325 " --> pdb=" O PRO H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 350 removed outlier: 4.143A pdb=" N VAL H 350 " --> pdb=" O SER H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 373 Processing helix chain 'H' and resid 374 through 376 No H-bonds generated for 'chain 'H' and resid 374 through 376' Processing helix chain 'H' and resid 379 through 388 Processing helix chain 'H' and resid 388 through 403 Processing helix chain 'H' and resid 408 through 429 removed outlier: 4.024A pdb=" N TRP H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 439 removed outlier: 3.574A pdb=" N TYR H 439 " --> pdb=" O PRO H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 466 removed outlier: 4.393A pdb=" N ASP H 455 " --> pdb=" O ALA H 451 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Proline residue: H 460 - end of helix Processing helix chain 'H' and resid 467 through 471 removed outlier: 3.923A pdb=" N LEU H 471 " --> pdb=" O LEU H 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 55 removed outlier: 3.660A pdb=" N VAL I 38 " --> pdb=" O THR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 88 Processing helix chain 'J' and resid 93 through 130 removed outlier: 3.548A pdb=" N VAL J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.528A pdb=" N SER J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 212 removed outlier: 3.905A pdb=" N LEU J 212 " --> pdb=" O VAL J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 238 removed outlier: 3.889A pdb=" N ALA J 224 " --> pdb=" O GLU J 220 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP J 238 " --> pdb=" O GLN J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 264 removed outlier: 3.525A pdb=" N TRP J 263 " --> pdb=" O TRP J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 293 Processing helix chain 'J' and resid 386 through 398 Processing helix chain 'G' and resid 2 through 17 Processing helix chain 'G' and resid 27 through 41 removed outlier: 3.777A pdb=" N ILE G 38 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 63 removed outlier: 3.592A pdb=" N ASN G 63 " --> pdb=" O MET G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 131 through 137 removed outlier: 3.507A pdb=" N ALA G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 162 removed outlier: 3.572A pdb=" N GLN G 162 " --> pdb=" O HIS G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 212 Processing helix chain 'G' and resid 265 through 269 Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.716A pdb=" N ALA D 6 " --> pdb=" O THR D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 41 removed outlier: 3.668A pdb=" N ILE D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 89 through 95 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 265 through 269 Processing sheet with id=AA1, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.409A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.896A pdb=" N LEU C 94 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA C 13 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU C 96 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU C 15 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ALA C 98 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 23 through 24 removed outlier: 3.577A pdb=" N ILE F 24 " --> pdb=" O LYS F 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AA5, first strand: chain 'F' and resid 202 through 204 Processing sheet with id=AA6, first strand: chain 'F' and resid 244 through 249 removed outlier: 6.735A pdb=" N GLY F 245 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL F 317 " --> pdb=" O GLY F 245 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA F 247 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU F 314 " --> pdb=" O THR F 338 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE F 340 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL F 316 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ARG F 342 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU F 318 " --> pdb=" O ARG F 342 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY F 219 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 360 " --> pdb=" O THR F 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 67 through 71 removed outlier: 8.641A pdb=" N LEU E 94 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA E 13 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU E 96 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU E 15 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA E 98 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU E 24 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 110 " --> pdb=" O LEU E 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 25 through 30 removed outlier: 8.864A pdb=" N LEU H 94 " --> pdb=" O ARG H 11 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA H 13 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU H 96 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU H 15 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ALA H 98 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 4 through 5 removed outlier: 6.250A pdb=" N LEU J 4 " --> pdb=" O ASP J 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AB2, first strand: chain 'J' and resid 158 through 164 removed outlier: 5.385A pdb=" N ARG J 159 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU J 207 " --> pdb=" O ARG J 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 339 through 343 removed outlier: 8.213A pdb=" N LEU J 360 " --> pdb=" O ARG J 214 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR J 216 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL J 362 " --> pdb=" O THR J 216 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 246 through 249 removed outlier: 6.628A pdb=" N ALA J 247 " --> pdb=" O VAL J 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 167 through 168 removed outlier: 3.670A pdb=" N LYS G 106 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 166 through 168 removed outlier: 3.918A pdb=" N LYS D 106 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL D 237 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL D 199 " --> pdb=" O VAL D 237 " (cutoff:3.500A) 1236 hydrogen bonds defined for protein. 3618 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: 6.59 Time building geometry restraints manager: 9.76 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: 7410 1.34 - 1.46: 4434 1.46 - 1.58: 10931 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 22871 Sorted by residual: bond pdb=" C ILE F 139 " pdb=" N PRO F 140 " ideal model delta sigma weight residual 1.337 1.392 -0.055 9.80e-03 1.04e+04 3.20e+01 bond pdb=" CB VAL H 363 " pdb=" CG1 VAL H 363 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CA THR D 103 " pdb=" CB THR D 103 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.94e+00 bond pdb=" CB PRO C 199 " pdb=" CG PRO C 199 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" C ILE J 139 " pdb=" N PRO J 140 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.25e-02 6.40e+03 2.88e+00 ... (remaining 22866 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.99: 744 105.99 - 113.39: 13335 113.39 - 120.79: 10254 120.79 - 128.18: 6726 128.18 - 135.58: 258 Bond angle restraints: 31317 Sorted by residual: angle pdb=" N VAL H 270 " pdb=" CA VAL H 270 " pdb=" C VAL H 270 " ideal model delta sigma weight residual 113.71 106.62 7.09 9.50e-01 1.11e+00 5.57e+01 angle pdb=" N ILE C 433 " pdb=" CA ILE C 433 " pdb=" C ILE C 433 " ideal model delta sigma weight residual 112.96 107.00 5.96 1.00e+00 1.00e+00 3.56e+01 angle pdb=" C ASP E 211 " pdb=" N PHE E 212 " pdb=" CA PHE E 212 " ideal model delta sigma weight residual 121.54 131.35 -9.81 1.91e+00 2.74e-01 2.64e+01 angle pdb=" C ALA F 323 " pdb=" N ASP F 324 " pdb=" CA ASP F 324 " ideal model delta sigma weight residual 121.80 133.27 -11.47 2.44e+00 1.68e-01 2.21e+01 angle pdb=" N VAL B 343 " pdb=" CA VAL B 343 " pdb=" C VAL B 343 " ideal model delta sigma weight residual 113.42 107.98 5.44 1.17e+00 7.31e-01 2.16e+01 ... (remaining 31312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 12289 18.02 - 36.03: 1167 36.03 - 54.05: 189 54.05 - 72.06: 28 72.06 - 90.08: 13 Dihedral angle restraints: 13686 sinusoidal: 5053 harmonic: 8633 Sorted by residual: dihedral pdb=" CA GLY D 171 " pdb=" C GLY D 171 " pdb=" N VAL D 172 " pdb=" CA VAL D 172 " ideal model delta harmonic sigma weight residual -180.00 -139.62 -40.38 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" CA VAL E 99 " pdb=" C VAL E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta harmonic sigma weight residual -180.00 -143.24 -36.76 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" CA GLY G 171 " pdb=" C GLY G 171 " pdb=" N VAL G 172 " pdb=" CA VAL G 172 " ideal model delta harmonic sigma weight residual -180.00 -147.38 -32.62 0 5.00e+00 4.00e-02 4.26e+01 ... (remaining 13683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3113 0.066 - 0.133: 639 0.133 - 0.199: 118 0.199 - 0.266: 21 0.266 - 0.332: 5 Chirality restraints: 3896 Sorted by residual: chirality pdb=" CB THR F 216 " pdb=" CA THR F 216 " pdb=" OG1 THR F 216 " pdb=" CG2 THR F 216 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB THR D 117 " pdb=" CA THR D 117 " pdb=" OG1 THR D 117 " pdb=" CG2 THR D 117 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG J 357 " pdb=" N ARG J 357 " pdb=" C ARG J 357 " pdb=" CB ARG J 357 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3893 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 306 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO H 307 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 307 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 307 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 332 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C THR B 332 " -0.049 2.00e-02 2.50e+03 pdb=" O THR B 332 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY B 333 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 331 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C GLN E 331 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN E 331 " 0.018 2.00e-02 2.50e+03 pdb=" N THR E 332 " 0.016 2.00e-02 2.50e+03 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5164 2.79 - 3.32: 20854 3.32 - 3.84: 36566 3.84 - 4.37: 39441 4.37 - 4.90: 68642 Nonbonded interactions: 170667 Sorted by model distance: nonbonded pdb=" OG1 THR D 174 " pdb=" O LEU D 176 " model vdw 2.259 2.440 nonbonded pdb=" OG SER H 228 " pdb=" O PHE H 244 " model vdw 2.271 2.440 nonbonded pdb=" O ALA J 233 " pdb=" OG1 THR J 237 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR C 82 " pdb=" OG1 THR C 85 " model vdw 2.293 2.440 nonbonded pdb=" OG SER G 139 " pdb=" O ARG G 141 " model vdw 2.302 2.440 ... (remaining 170662 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 'B' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 471)) selection = (chain 'C' and (resid 8 through 294 or resid 316 through 471)) selection = (chain 'E' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 471)) selection = (chain 'H' and (resid 8 through 294 or resid 316 through 471)) } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'F' and (resid 2 through 32 or resid 92 through 297 or resid 311 through \ 401)) selection = (chain 'J' and resid 2 through 401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.91 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 16.470 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 59.000 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.006 0.085 22871 Z= 0.406 Angle : 1.039 11.475 31317 Z= 0.553 Chirality : 0.058 0.332 3896 Planarity : 0.008 0.075 3952 Dihedral : 14.455 90.078 8062 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.50 % Favored : 90.29 % Rotamer: Outliers : 0.26 % Allowed : 12.42 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.12), residues: 2936 helix: -2.68 (0.09), residues: 1571 sheet: -1.70 (0.28), residues: 271 loop : -3.67 (0.16), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 231 HIS 0.006 0.001 HIS F 341 PHE 0.014 0.002 PHE B 165 TYR 0.015 0.002 TYR F 104 ARG 0.009 0.001 ARG J 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 461 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8290 (ttp) cc_final: 0.7984 (ttm) REVERT: B 256 LEU cc_start: 0.8509 (tt) cc_final: 0.7901 (mm) REVERT: B 285 GLN cc_start: 0.7493 (mt0) cc_final: 0.7253 (tt0) REVERT: B 328 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8172 (tm-30) REVERT: B 360 TRP cc_start: 0.6944 (m100) cc_final: 0.6732 (m100) REVERT: C 273 CYS cc_start: 0.7692 (m) cc_final: 0.7282 (m) REVERT: C 292 MET cc_start: 0.6916 (mtt) cc_final: 0.6611 (mtt) REVERT: C 378 ASP cc_start: 0.8278 (t0) cc_final: 0.7965 (t0) REVERT: F 231 TRP cc_start: 0.8708 (p90) cc_final: 0.8438 (p90) REVERT: E 43 GLN cc_start: 0.8287 (mt0) cc_final: 0.8039 (mt0) REVERT: E 123 ARG cc_start: 0.5681 (tpt90) cc_final: 0.5116 (ttm-80) REVERT: E 391 TYR cc_start: 0.8401 (t80) cc_final: 0.8031 (t80) REVERT: E 430 ASN cc_start: 0.6262 (t0) cc_final: 0.5550 (m110) REVERT: E 432 LYS cc_start: 0.6788 (tttt) cc_final: 0.6363 (pttm) REVERT: H 27 MET cc_start: 0.6456 (tpt) cc_final: 0.6091 (tpp) REVERT: H 123 ARG cc_start: 0.7621 (mmt180) cc_final: 0.7347 (mpt180) REVERT: H 232 MET cc_start: 0.9122 (ttp) cc_final: 0.8862 (ttp) REVERT: H 420 LEU cc_start: 0.8899 (mt) cc_final: 0.8648 (mp) REVERT: J 29 GLN cc_start: 0.8039 (mt0) cc_final: 0.7588 (tt0) REVERT: J 113 ASP cc_start: 0.7929 (m-30) cc_final: 0.7615 (t0) REVERT: J 357 ARG cc_start: 0.8431 (ptp-170) cc_final: 0.8206 (mtt90) REVERT: G 1 MET cc_start: 0.4974 (ptm) cc_final: 0.4530 (ptt) REVERT: G 55 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7225 (ttm-80) REVERT: G 161 GLU cc_start: 0.8405 (pp20) cc_final: 0.8196 (pp20) REVERT: G 173 ASP cc_start: 0.7699 (t0) cc_final: 0.7451 (t70) REVERT: G 211 GLU cc_start: 0.6177 (tt0) cc_final: 0.5701 (pt0) REVERT: D 47 MET cc_start: 0.1131 (ttt) cc_final: -0.0308 (ptt) REVERT: D 108 ARG cc_start: 0.6345 (ttm170) cc_final: 0.5695 (ttm170) REVERT: D 225 GLU cc_start: 0.6645 (tt0) cc_final: 0.6341 (tt0) REVERT: D 233 PRO cc_start: 0.7255 (Cg_endo) cc_final: 0.6949 (Cg_exo) outliers start: 6 outliers final: 3 residues processed: 465 average time/residue: 0.3384 time to fit residues: 239.1151 Evaluate side-chains 321 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 318 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 77 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 233 optimal weight: 0.4980 chunk 90 optimal weight: 0.3980 chunk 142 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 270 optimal weight: 7.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 67 GLN B 183 ASN B 330 HIS C 331 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 341 HIS E 43 GLN E 47 GLN E 354 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN H 389 HIS I 67 GLN J 122 GLN J 145 GLN J 187 HIS G 63 ASN D 74 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22871 Z= 0.182 Angle : 0.657 9.394 31317 Z= 0.325 Chirality : 0.041 0.181 3896 Planarity : 0.006 0.070 3952 Dihedral : 5.401 43.174 3248 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.30 % Favored : 90.60 % Rotamer: Outliers : 2.74 % Allowed : 17.24 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.15), residues: 2936 helix: -0.71 (0.12), residues: 1604 sheet: -1.39 (0.30), residues: 256 loop : -3.23 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 231 HIS 0.008 0.001 HIS F 341 PHE 0.010 0.001 PHE E 469 TYR 0.013 0.001 TYR E 361 ARG 0.005 0.000 ARG J 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 387 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 LEU cc_start: 0.8439 (tt) cc_final: 0.7947 (mm) REVERT: B 285 GLN cc_start: 0.7669 (mt0) cc_final: 0.7420 (tt0) REVERT: B 422 LEU cc_start: 0.8535 (tp) cc_final: 0.8217 (tp) REVERT: C 127 TRP cc_start: 0.8584 (t-100) cc_final: 0.8370 (t-100) REVERT: C 292 MET cc_start: 0.6900 (mtt) cc_final: 0.6580 (mtt) REVERT: C 378 ASP cc_start: 0.8133 (t0) cc_final: 0.7921 (t0) REVERT: C 465 LEU cc_start: 0.8845 (tp) cc_final: 0.8366 (tp) REVERT: F 262 LYS cc_start: 0.7736 (mttt) cc_final: 0.7520 (mtpp) REVERT: F 288 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7013 (tp30) REVERT: E 140 LEU cc_start: 0.9105 (tp) cc_final: 0.8680 (tt) REVERT: E 391 TYR cc_start: 0.8381 (t80) cc_final: 0.8011 (t80) REVERT: E 430 ASN cc_start: 0.6284 (t0) cc_final: 0.5613 (m110) REVERT: E 432 LYS cc_start: 0.6746 (tttt) cc_final: 0.6322 (pttm) REVERT: E 446 MET cc_start: 0.5320 (mmm) cc_final: 0.4678 (ttp) REVERT: H 417 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8261 (tt) REVERT: H 430 ASN cc_start: 0.7482 (t0) cc_final: 0.7116 (t0) REVERT: J 29 GLN cc_start: 0.7986 (mt0) cc_final: 0.7516 (tt0) REVERT: J 113 ASP cc_start: 0.7854 (m-30) cc_final: 0.7603 (t0) REVERT: J 399 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7339 (ttm110) REVERT: G 1 MET cc_start: 0.5015 (ptm) cc_final: 0.4578 (ptt) REVERT: G 4 ARG cc_start: 0.5955 (mmt-90) cc_final: 0.3904 (mmm160) REVERT: G 55 ARG cc_start: 0.7535 (ttm170) cc_final: 0.7191 (ttm-80) REVERT: G 99 ARG cc_start: 0.8125 (ptp-170) cc_final: 0.7569 (ptp-170) REVERT: G 211 GLU cc_start: 0.6259 (tt0) cc_final: 0.5679 (pt0) REVERT: G 278 LEU cc_start: 0.8017 (mt) cc_final: 0.7662 (tt) REVERT: D 47 MET cc_start: 0.1182 (ttt) cc_final: -0.0262 (ptt) REVERT: D 145 GLN cc_start: 0.7465 (tp40) cc_final: 0.7196 (tp40) REVERT: D 161 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 233 PRO cc_start: 0.7149 (Cg_endo) cc_final: 0.6883 (Cg_exo) outliers start: 63 outliers final: 38 residues processed: 427 average time/residue: 0.3032 time to fit residues: 205.5985 Evaluate side-chains 361 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 321 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 348 ASN Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 399 ARG Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 225 optimal weight: 0.0980 chunk 184 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 67 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN E 47 GLN E 331 GLN H 331 GLN J 371 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22871 Z= 0.328 Angle : 0.725 8.748 31317 Z= 0.360 Chirality : 0.043 0.210 3896 Planarity : 0.006 0.068 3952 Dihedral : 5.437 56.595 3248 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.25 % Favored : 89.68 % Rotamer: Outliers : 4.08 % Allowed : 19.19 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2936 helix: -0.08 (0.13), residues: 1605 sheet: -1.40 (0.30), residues: 270 loop : -3.06 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 293 HIS 0.005 0.001 HIS F 392 PHE 0.015 0.001 PHE B 165 TYR 0.015 0.002 TYR J 104 ARG 0.008 0.000 ARG E 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 335 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8570 (ttp) cc_final: 0.8142 (ttm) REVERT: C 127 TRP cc_start: 0.8721 (t-100) cc_final: 0.8497 (t-100) REVERT: C 292 MET cc_start: 0.7116 (mtt) cc_final: 0.6844 (mtt) REVERT: C 465 LEU cc_start: 0.8864 (tp) cc_final: 0.8454 (tp) REVERT: F 351 GLN cc_start: 0.5523 (OUTLIER) cc_final: 0.5193 (pt0) REVERT: E 27 MET cc_start: 0.7941 (ptp) cc_final: 0.7707 (ptp) REVERT: E 391 TYR cc_start: 0.8414 (t80) cc_final: 0.8026 (t80) REVERT: E 430 ASN cc_start: 0.6462 (t0) cc_final: 0.5797 (m110) REVERT: E 432 LYS cc_start: 0.6776 (tttt) cc_final: 0.6347 (pttm) REVERT: E 443 MET cc_start: 0.4702 (mtp) cc_final: 0.4441 (mtp) REVERT: E 446 MET cc_start: 0.5517 (mmm) cc_final: 0.4878 (ttp) REVERT: E 468 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2749 (tt) REVERT: H 417 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8416 (tt) REVERT: H 430 ASN cc_start: 0.7602 (t0) cc_final: 0.7166 (t0) REVERT: H 441 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8064 (mm) REVERT: I 45 MET cc_start: 0.8465 (tpp) cc_final: 0.8205 (tpp) REVERT: J 29 GLN cc_start: 0.8052 (mt0) cc_final: 0.7603 (tt0) REVERT: J 113 ASP cc_start: 0.7930 (m-30) cc_final: 0.7645 (t0) REVERT: J 376 GLN cc_start: 0.7623 (tt0) cc_final: 0.7352 (tm-30) REVERT: J 399 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7372 (ttm110) REVERT: G 1 MET cc_start: 0.5167 (ptm) cc_final: 0.4786 (ptt) REVERT: G 4 ARG cc_start: 0.6190 (mmt-90) cc_final: 0.4125 (mmm160) REVERT: G 89 GLN cc_start: 0.7497 (pp30) cc_final: 0.6810 (pp30) REVERT: G 161 GLU cc_start: 0.8333 (pp20) cc_final: 0.8104 (pp20) REVERT: G 225 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7440 (mt-10) REVERT: D 47 MET cc_start: 0.1035 (ttt) cc_final: 0.0122 (ptt) REVERT: D 161 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8230 (tm-30) outliers start: 94 outliers final: 62 residues processed: 388 average time/residue: 0.3036 time to fit residues: 187.4298 Evaluate side-chains 362 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 295 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 341 HIS Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 433 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 399 ARG Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 129 optimal weight: 0.0870 chunk 182 optimal weight: 0.0970 chunk 272 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 257 optimal weight: 0.0870 chunk 77 optimal weight: 0.3980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS C 285 GLN C 331 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN D 158 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22871 Z= 0.163 Angle : 0.620 9.472 31317 Z= 0.305 Chirality : 0.040 0.168 3896 Planarity : 0.005 0.064 3952 Dihedral : 4.839 30.006 3246 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.75 % Favored : 91.14 % Rotamer: Outliers : 2.95 % Allowed : 21.32 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2936 helix: 0.50 (0.13), residues: 1606 sheet: -1.08 (0.30), residues: 270 loop : -2.90 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 231 HIS 0.003 0.001 HIS J 163 PHE 0.013 0.001 PHE D 48 TYR 0.010 0.001 TYR F 104 ARG 0.005 0.000 ARG D 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 349 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8236 (ttp) cc_final: 0.7913 (ttm) REVERT: B 289 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8522 (tt) REVERT: C 292 MET cc_start: 0.7199 (mtt) cc_final: 0.6914 (mtt) REVERT: C 465 LEU cc_start: 0.8877 (tp) cc_final: 0.8481 (tp) REVERT: F 216 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7214 (t) REVERT: F 288 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7059 (tp30) REVERT: F 320 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6611 (m-30) REVERT: E 245 THR cc_start: 0.9205 (t) cc_final: 0.8928 (m) REVERT: E 391 TYR cc_start: 0.8251 (t80) cc_final: 0.7946 (t80) REVERT: E 430 ASN cc_start: 0.6314 (t0) cc_final: 0.5685 (m110) REVERT: E 432 LYS cc_start: 0.6779 (tttt) cc_final: 0.6287 (pttm) REVERT: E 443 MET cc_start: 0.4764 (mtp) cc_final: 0.4493 (mtp) REVERT: E 446 MET cc_start: 0.5527 (mmm) cc_final: 0.4871 (ttp) REVERT: H 232 MET cc_start: 0.9109 (ttp) cc_final: 0.8864 (ttp) REVERT: H 417 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8266 (tt) REVERT: H 430 ASN cc_start: 0.7525 (t0) cc_final: 0.7113 (t0) REVERT: H 441 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7851 (mm) REVERT: J 29 GLN cc_start: 0.7968 (mt0) cc_final: 0.7530 (tt0) REVERT: J 113 ASP cc_start: 0.7859 (m-30) cc_final: 0.7626 (t0) REVERT: J 399 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7343 (ttm110) REVERT: G 1 MET cc_start: 0.5075 (ptm) cc_final: 0.4696 (ptt) REVERT: G 4 ARG cc_start: 0.6231 (mmt-90) cc_final: 0.4056 (mmm160) REVERT: G 89 GLN cc_start: 0.7610 (pp30) cc_final: 0.6844 (pp30) REVERT: D 47 MET cc_start: 0.0103 (ttt) cc_final: -0.0762 (ptt) REVERT: D 106 LYS cc_start: 0.7397 (pptt) cc_final: 0.5882 (tmmt) REVERT: D 131 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8121 (p0) REVERT: D 161 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8232 (tm-30) REVERT: D 233 PRO cc_start: 0.7194 (Cg_endo) cc_final: 0.6890 (Cg_exo) outliers start: 68 outliers final: 40 residues processed: 391 average time/residue: 0.3132 time to fit residues: 200.8590 Evaluate side-chains 360 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 313 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 348 ASN Chi-restraints excluded: chain J residue 399 ARG Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22871 Z= 0.285 Angle : 0.683 9.360 31317 Z= 0.335 Chirality : 0.042 0.219 3896 Planarity : 0.005 0.064 3952 Dihedral : 4.919 31.368 3246 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.78 % Favored : 90.16 % Rotamer: Outliers : 4.30 % Allowed : 22.45 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2936 helix: 0.63 (0.13), residues: 1606 sheet: -1.02 (0.31), residues: 258 loop : -2.84 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 293 HIS 0.004 0.001 HIS F 392 PHE 0.027 0.001 PHE C 77 TYR 0.013 0.001 TYR F 104 ARG 0.004 0.000 ARG F 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 309 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8504 (ttp) cc_final: 0.8097 (ttm) REVERT: B 289 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 292 MET cc_start: 0.7100 (mtt) cc_final: 0.6839 (mtt) REVERT: C 465 LEU cc_start: 0.8903 (tp) cc_final: 0.8566 (tp) REVERT: F 216 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7463 (t) REVERT: F 351 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.4879 (pt0) REVERT: E 140 LEU cc_start: 0.9188 (tp) cc_final: 0.8789 (tt) REVERT: E 391 TYR cc_start: 0.8372 (t80) cc_final: 0.8013 (t80) REVERT: E 430 ASN cc_start: 0.6375 (t0) cc_final: 0.5757 (m110) REVERT: E 432 LYS cc_start: 0.6825 (tttt) cc_final: 0.6386 (pttm) REVERT: E 446 MET cc_start: 0.5269 (mmm) cc_final: 0.4646 (ttp) REVERT: H 417 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8337 (tt) REVERT: H 441 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8089 (mm) REVERT: I 45 MET cc_start: 0.8487 (tpp) cc_final: 0.8155 (tpp) REVERT: J 29 GLN cc_start: 0.8067 (mt0) cc_final: 0.7620 (tt0) REVERT: J 113 ASP cc_start: 0.7987 (m-30) cc_final: 0.7667 (t0) REVERT: J 399 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7406 (ttm110) REVERT: G 1 MET cc_start: 0.4825 (ptm) cc_final: 0.4486 (ptt) REVERT: G 4 ARG cc_start: 0.6374 (mmt-90) cc_final: 0.4160 (mmm160) REVERT: G 22 GLN cc_start: 0.6934 (mp10) cc_final: 0.6490 (tp40) REVERT: G 89 GLN cc_start: 0.7640 (pp30) cc_final: 0.7008 (pp30) REVERT: D 47 MET cc_start: 0.0455 (ttt) cc_final: -0.0385 (ptt) REVERT: D 131 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8155 (p0) REVERT: D 161 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8238 (tm-30) outliers start: 99 outliers final: 71 residues processed: 371 average time/residue: 0.2937 time to fit residues: 179.3842 Evaluate side-chains 371 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 293 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 341 HIS Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 397 LEU Chi-restraints excluded: chain J residue 399 ARG Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 133 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22871 Z= 0.345 Angle : 0.733 9.206 31317 Z= 0.362 Chirality : 0.043 0.199 3896 Planarity : 0.006 0.064 3952 Dihedral : 5.208 30.215 3246 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.76 % Favored : 89.17 % Rotamer: Outliers : 5.38 % Allowed : 22.67 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2936 helix: 0.59 (0.13), residues: 1598 sheet: -1.19 (0.32), residues: 274 loop : -2.82 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 127 HIS 0.004 0.001 HIS E 154 PHE 0.021 0.002 PHE C 77 TYR 0.016 0.002 TYR J 104 ARG 0.003 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 299 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8641 (ttp) cc_final: 0.8221 (ttm) REVERT: B 289 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8676 (tt) REVERT: C 127 TRP cc_start: 0.8688 (t-100) cc_final: 0.8475 (t-100) REVERT: C 145 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8808 (mm) REVERT: C 270 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7853 (t) REVERT: C 292 MET cc_start: 0.7275 (mtt) cc_final: 0.7002 (mtt) REVERT: C 465 LEU cc_start: 0.8894 (tp) cc_final: 0.8565 (tp) REVERT: F 216 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7571 (t) REVERT: F 288 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7226 (tp30) REVERT: F 320 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: F 351 GLN cc_start: 0.5364 (OUTLIER) cc_final: 0.5003 (pt0) REVERT: E 391 TYR cc_start: 0.8424 (t80) cc_final: 0.8008 (t80) REVERT: E 430 ASN cc_start: 0.6386 (t0) cc_final: 0.5983 (m110) REVERT: E 432 LYS cc_start: 0.6797 (tttt) cc_final: 0.6373 (pttm) REVERT: E 446 MET cc_start: 0.5522 (mmm) cc_final: 0.4799 (ttp) REVERT: H 417 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8476 (tt) REVERT: H 430 ASN cc_start: 0.7490 (t0) cc_final: 0.7184 (t0) REVERT: H 441 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8113 (mm) REVERT: I 45 MET cc_start: 0.8473 (tpp) cc_final: 0.8106 (tpp) REVERT: J 29 GLN cc_start: 0.8172 (mt0) cc_final: 0.7662 (tt0) REVERT: J 113 ASP cc_start: 0.7991 (m-30) cc_final: 0.7713 (t0) REVERT: J 399 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7491 (ttm110) REVERT: G 4 ARG cc_start: 0.6526 (mmt-90) cc_final: 0.4401 (mmm160) REVERT: G 22 GLN cc_start: 0.6992 (mp10) cc_final: 0.6463 (tp40) REVERT: G 89 GLN cc_start: 0.7782 (pp30) cc_final: 0.7290 (pp30) REVERT: D 47 MET cc_start: 0.0600 (ttt) cc_final: -0.0280 (ptm) REVERT: D 106 LYS cc_start: 0.7512 (pptt) cc_final: 0.7285 (pttt) REVERT: D 161 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8268 (tm-30) REVERT: D 276 GLU cc_start: 0.7664 (tp30) cc_final: 0.7424 (tp30) outliers start: 124 outliers final: 88 residues processed: 383 average time/residue: 0.2801 time to fit residues: 175.6884 Evaluate side-chains 374 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 277 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 341 HIS Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 397 LEU Chi-restraints excluded: chain J residue 399 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 287 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN C 285 GLN C 331 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN H 331 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22871 Z= 0.207 Angle : 0.655 11.635 31317 Z= 0.319 Chirality : 0.041 0.183 3896 Planarity : 0.005 0.069 3952 Dihedral : 4.875 27.577 3246 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.57 % Favored : 90.36 % Rotamer: Outliers : 4.34 % Allowed : 24.27 % Favored : 71.39 % 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: -0.82 (0.16), residues: 2936 helix: 0.87 (0.13), residues: 1608 sheet: -1.00 (0.32), residues: 264 loop : -2.70 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 231 HIS 0.003 0.001 HIS J 313 PHE 0.022 0.001 PHE C 77 TYR 0.012 0.001 TYR F 104 ARG 0.004 0.000 ARG F 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 313 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8458 (ttp) cc_final: 0.8059 (ttm) REVERT: B 289 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8628 (tt) REVERT: C 127 TRP cc_start: 0.8665 (t-100) cc_final: 0.8351 (t-100) REVERT: C 145 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8730 (mm) REVERT: C 270 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7774 (t) REVERT: C 292 MET cc_start: 0.7229 (mtt) cc_final: 0.6976 (mtt) REVERT: C 465 LEU cc_start: 0.8882 (tp) cc_final: 0.8550 (tp) REVERT: F 216 THR cc_start: 0.7515 (OUTLIER) cc_final: 0.7271 (t) REVERT: F 320 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: F 351 GLN cc_start: 0.5250 (OUTLIER) cc_final: 0.4911 (pt0) REVERT: E 245 THR cc_start: 0.8945 (t) cc_final: 0.8691 (m) REVERT: E 391 TYR cc_start: 0.8263 (t80) cc_final: 0.7916 (t80) REVERT: E 430 ASN cc_start: 0.6296 (t0) cc_final: 0.5946 (m110) REVERT: E 432 LYS cc_start: 0.6860 (tttt) cc_final: 0.6416 (pttm) REVERT: E 446 MET cc_start: 0.5421 (mmm) cc_final: 0.4757 (ttp) REVERT: H 232 MET cc_start: 0.9120 (ttp) cc_final: 0.8841 (ttp) REVERT: H 417 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8340 (tt) REVERT: H 430 ASN cc_start: 0.7531 (t0) cc_final: 0.7183 (t0) REVERT: H 441 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7997 (mm) REVERT: I 45 MET cc_start: 0.8454 (tpp) cc_final: 0.8111 (tpp) REVERT: J 29 GLN cc_start: 0.8025 (mt0) cc_final: 0.7579 (tt0) REVERT: J 399 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7521 (ttm110) REVERT: G 4 ARG cc_start: 0.6513 (mmt-90) cc_final: 0.4367 (mmm160) REVERT: G 22 GLN cc_start: 0.6928 (mp10) cc_final: 0.6425 (tp40) REVERT: G 89 GLN cc_start: 0.7762 (pp30) cc_final: 0.7306 (pp30) REVERT: D 47 MET cc_start: 0.0528 (ttt) cc_final: -0.0033 (ptm) REVERT: D 106 LYS cc_start: 0.7426 (pptt) cc_final: 0.7182 (pttt) REVERT: D 161 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8263 (tm-30) REVERT: D 276 GLU cc_start: 0.7674 (tp30) cc_final: 0.7381 (tp30) outliers start: 100 outliers final: 70 residues processed: 383 average time/residue: 0.2849 time to fit residues: 179.2757 Evaluate side-chains 375 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 296 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 341 HIS Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 348 ASN Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 399 ARG Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN C 331 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 22871 Z= 0.203 Angle : 0.652 10.144 31317 Z= 0.318 Chirality : 0.041 0.183 3896 Planarity : 0.005 0.070 3952 Dihedral : 4.780 27.428 3246 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.81 % Favored : 90.12 % Rotamer: Outliers : 4.39 % Allowed : 24.36 % Favored : 71.25 % 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: -0.68 (0.16), residues: 2936 helix: 1.00 (0.13), residues: 1603 sheet: -0.97 (0.32), residues: 264 loop : -2.66 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 231 HIS 0.003 0.001 HIS E 154 PHE 0.020 0.001 PHE C 77 TYR 0.012 0.001 TYR F 104 ARG 0.005 0.000 ARG F 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 308 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8485 (ttp) cc_final: 0.8090 (ttm) REVERT: B 289 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 127 TRP cc_start: 0.8668 (t-100) cc_final: 0.8343 (t-100) REVERT: C 270 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7824 (t) REVERT: C 292 MET cc_start: 0.7227 (mtt) cc_final: 0.6961 (mtt) REVERT: C 465 LEU cc_start: 0.8851 (tp) cc_final: 0.8489 (tp) REVERT: F 216 THR cc_start: 0.7509 (OUTLIER) cc_final: 0.7263 (t) REVERT: F 288 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7083 (tp30) REVERT: F 320 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: F 351 GLN cc_start: 0.5409 (OUTLIER) cc_final: 0.5059 (pt0) REVERT: E 245 THR cc_start: 0.8947 (t) cc_final: 0.8701 (m) REVERT: E 391 TYR cc_start: 0.8288 (t80) cc_final: 0.7937 (t80) REVERT: E 430 ASN cc_start: 0.6300 (t0) cc_final: 0.5948 (m110) REVERT: E 432 LYS cc_start: 0.6803 (tttt) cc_final: 0.6397 (pttm) REVERT: E 446 MET cc_start: 0.5341 (mmm) cc_final: 0.4656 (ttp) REVERT: H 232 MET cc_start: 0.9123 (ttp) cc_final: 0.8833 (ttp) REVERT: H 417 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8316 (tt) REVERT: H 430 ASN cc_start: 0.7532 (t0) cc_final: 0.7173 (t0) REVERT: H 441 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7985 (mm) REVERT: I 45 MET cc_start: 0.8471 (tpp) cc_final: 0.8118 (tpp) REVERT: J 29 GLN cc_start: 0.7948 (mt0) cc_final: 0.7512 (tt0) REVERT: J 399 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7505 (ttm110) REVERT: G 4 ARG cc_start: 0.6447 (mmt-90) cc_final: 0.4343 (mmm160) REVERT: G 22 GLN cc_start: 0.6883 (mp10) cc_final: 0.6443 (tp40) REVERT: D 47 MET cc_start: 0.0585 (ttt) cc_final: 0.0030 (ptm) REVERT: D 106 LYS cc_start: 0.7401 (pptt) cc_final: 0.7176 (pttt) REVERT: D 131 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8106 (p0) REVERT: D 161 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8268 (tm-30) REVERT: D 199 VAL cc_start: 0.7723 (p) cc_final: 0.7504 (p) REVERT: D 276 GLU cc_start: 0.7658 (tp30) cc_final: 0.7101 (tp30) outliers start: 101 outliers final: 74 residues processed: 380 average time/residue: 0.2897 time to fit residues: 180.4317 Evaluate side-chains 379 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 296 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 341 HIS Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain H residue 459 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 348 ASN Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 399 ARG Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 0.2980 chunk 275 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 116 optimal weight: 0.0170 chunk 210 optimal weight: 3.9990 chunk 82 optimal weight: 0.0770 chunk 241 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 chunk 266 optimal weight: 0.6980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN C 331 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 22871 Z= 0.176 Angle : 0.643 9.796 31317 Z= 0.312 Chirality : 0.041 0.275 3896 Planarity : 0.005 0.071 3952 Dihedral : 4.609 28.148 3246 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.03 % Favored : 90.91 % Rotamer: Outliers : 3.56 % Allowed : 25.40 % Favored : 71.04 % 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: -0.52 (0.16), residues: 2936 helix: 1.14 (0.13), residues: 1601 sheet: -0.86 (0.32), residues: 264 loop : -2.61 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 231 HIS 0.005 0.001 HIS C 330 PHE 0.020 0.001 PHE D 226 TYR 0.014 0.001 TYR J 281 ARG 0.005 0.000 ARG F 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 310 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8354 (ttp) cc_final: 0.7971 (ttm) REVERT: B 289 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 127 TRP cc_start: 0.8626 (t-100) cc_final: 0.8317 (t-100) REVERT: C 270 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7757 (t) REVERT: C 292 MET cc_start: 0.7174 (mtt) cc_final: 0.6923 (mtt) REVERT: C 462 MET cc_start: 0.7845 (tpp) cc_final: 0.7293 (tpt) REVERT: C 465 LEU cc_start: 0.8795 (tp) cc_final: 0.8408 (tp) REVERT: F 216 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7325 (t) REVERT: F 288 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7081 (tp30) REVERT: E 245 THR cc_start: 0.8963 (t) cc_final: 0.8639 (m) REVERT: E 391 TYR cc_start: 0.8225 (t80) cc_final: 0.7943 (t80) REVERT: E 430 ASN cc_start: 0.6208 (t0) cc_final: 0.5871 (m110) REVERT: E 432 LYS cc_start: 0.6774 (tttt) cc_final: 0.6311 (pttm) REVERT: E 446 MET cc_start: 0.5354 (mmm) cc_final: 0.4653 (ttp) REVERT: H 232 MET cc_start: 0.9110 (ttp) cc_final: 0.8838 (ttp) REVERT: H 417 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8275 (tt) REVERT: H 430 ASN cc_start: 0.7459 (t0) cc_final: 0.7198 (t0) REVERT: I 45 MET cc_start: 0.8452 (tpp) cc_final: 0.8057 (tpp) REVERT: J 96 GLU cc_start: 0.7230 (tp30) cc_final: 0.7029 (tp30) REVERT: G 4 ARG cc_start: 0.6567 (mmt-90) cc_final: 0.4356 (mmm160) REVERT: G 22 GLN cc_start: 0.6853 (mp10) cc_final: 0.6426 (tp40) REVERT: D 47 MET cc_start: 0.0416 (ttt) cc_final: -0.0020 (ptm) REVERT: D 106 LYS cc_start: 0.7368 (pptt) cc_final: 0.7054 (pttt) REVERT: D 131 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8121 (p0) REVERT: D 161 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 199 VAL cc_start: 0.7515 (p) cc_final: 0.7312 (p) REVERT: D 276 GLU cc_start: 0.7733 (tp30) cc_final: 0.7050 (tp30) outliers start: 82 outliers final: 65 residues processed: 370 average time/residue: 0.2854 time to fit residues: 174.0523 Evaluate side-chains 371 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 301 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 348 ASN Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 0.9990 chunk 283 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 196 optimal weight: 0.0570 chunk 296 optimal weight: 0.6980 chunk 273 optimal weight: 0.7980 chunk 236 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 22871 Z= 0.191 Angle : 0.648 10.205 31317 Z= 0.315 Chirality : 0.041 0.263 3896 Planarity : 0.005 0.071 3952 Dihedral : 4.564 28.622 3246 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.33 % Favored : 90.60 % Rotamer: Outliers : 3.52 % Allowed : 25.36 % Favored : 71.12 % 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: -0.44 (0.16), residues: 2936 helix: 1.21 (0.13), residues: 1603 sheet: -0.83 (0.32), residues: 264 loop : -2.58 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 231 HIS 0.007 0.001 HIS C 330 PHE 0.020 0.001 PHE B 165 TYR 0.012 0.001 TYR C 407 ARG 0.008 0.000 ARG F 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 307 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8439 (mmm) cc_final: 0.8228 (tpp) REVERT: B 232 MET cc_start: 0.8420 (ttp) cc_final: 0.8040 (ttm) REVERT: B 289 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8632 (tt) REVERT: C 126 GLN cc_start: 0.7946 (tp40) cc_final: 0.7571 (tp40) REVERT: C 127 TRP cc_start: 0.8629 (t-100) cc_final: 0.8358 (t-100) REVERT: C 270 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7783 (t) REVERT: C 292 MET cc_start: 0.7153 (mtt) cc_final: 0.6912 (mtt) REVERT: C 465 LEU cc_start: 0.8788 (tp) cc_final: 0.8423 (tp) REVERT: F 288 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7087 (tp30) REVERT: F 320 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: F 351 GLN cc_start: 0.5324 (OUTLIER) cc_final: 0.4970 (pt0) REVERT: E 232 MET cc_start: 0.8913 (ttp) cc_final: 0.8641 (ttp) REVERT: E 245 THR cc_start: 0.8952 (t) cc_final: 0.8633 (m) REVERT: E 391 TYR cc_start: 0.8284 (t80) cc_final: 0.7994 (t80) REVERT: E 430 ASN cc_start: 0.6227 (t0) cc_final: 0.5870 (m110) REVERT: E 432 LYS cc_start: 0.6779 (tttt) cc_final: 0.6370 (pttm) REVERT: E 446 MET cc_start: 0.5364 (mmm) cc_final: 0.4655 (ttp) REVERT: H 232 MET cc_start: 0.9090 (ttp) cc_final: 0.8822 (ttp) REVERT: H 417 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8302 (tt) REVERT: H 430 ASN cc_start: 0.7466 (t0) cc_final: 0.7195 (t0) REVERT: I 45 MET cc_start: 0.8476 (tpp) cc_final: 0.8097 (tpp) REVERT: J 96 GLU cc_start: 0.7271 (tp30) cc_final: 0.7052 (tp30) REVERT: G 4 ARG cc_start: 0.6684 (mmt-90) cc_final: 0.4516 (mmm160) REVERT: G 22 GLN cc_start: 0.6864 (mp10) cc_final: 0.6430 (tp40) REVERT: G 40 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6569 (tt) REVERT: D 47 MET cc_start: 0.0372 (ttt) cc_final: 0.0024 (ptm) REVERT: D 106 LYS cc_start: 0.7281 (pptt) cc_final: 0.7016 (pttt) REVERT: D 276 GLU cc_start: 0.7717 (tp30) cc_final: 0.7006 (tp30) outliers start: 81 outliers final: 66 residues processed: 370 average time/residue: 0.2870 time to fit residues: 174.0982 Evaluate side-chains 366 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 294 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 320 ASP Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 348 ASN Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 0.0980 chunk 251 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109723 restraints weight = 51032.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111487 restraints weight = 35288.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112349 restraints weight = 24599.627| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22871 Z= 0.196 Angle : 0.647 9.440 31317 Z= 0.315 Chirality : 0.041 0.254 3896 Planarity : 0.005 0.070 3952 Dihedral : 4.513 27.411 3246 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.50 % Favored : 90.43 % Rotamer: Outliers : 3.60 % Allowed : 25.40 % Favored : 70.99 % 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: -0.39 (0.16), residues: 2936 helix: 1.24 (0.13), residues: 1609 sheet: -0.84 (0.32), residues: 264 loop : -2.54 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 231 HIS 0.003 0.001 HIS E 389 PHE 0.020 0.001 PHE B 165 TYR 0.012 0.001 TYR C 407 ARG 0.003 0.000 ARG F 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4637.37 seconds wall clock time: 84 minutes 16.97 seconds (5056.97 seconds total)