Starting phenix.real_space_refine on Mon Jul 22 16:50:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pto_17876/07_2024/8pto_17876.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pto_17876/07_2024/8pto_17876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pto_17876/07_2024/8pto_17876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pto_17876/07_2024/8pto_17876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pto_17876/07_2024/8pto_17876.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pto_17876/07_2024/8pto_17876.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 97 5.16 5 C 11989 2.51 5 N 3372 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19124 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "c" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "d" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "a" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.13, per 1000 atoms: 0.58 Number of scatterers: 19124 At special positions: 0 Unit cell: (118.144, 134.784, 161.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 6 15.00 O 3660 8.00 N 3372 7.00 C 11989 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: 6.83 Conformation dependent library (CDL) restraints added in 3.3 seconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4522 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 23 sheets defined 46.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.630A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.655A pdb=" N ASN A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.893A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.676A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 285 through 289 removed outlier: 4.197A pdb=" N VAL A 289 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.043A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 removed outlier: 4.277A pdb=" N GLY A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.146A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 removed outlier: 3.623A pdb=" N GLN A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.588A pdb=" N MET A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.684A pdb=" N LEU B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.744A pdb=" N ARG B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 4.280A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.504A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 336 through 339 removed outlier: 4.495A pdb=" N GLY B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 336 through 339' Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.260A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.518A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.563A pdb=" N MET B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.803A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.114A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 removed outlier: 3.566A pdb=" N THR C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'C' and resid 334 through 339 removed outlier: 5.369A pdb=" N GLY C 337 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 338 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 334 through 339' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.305A pdb=" N LEU C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.597A pdb=" N MET C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.565A pdb=" N LEU D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.297A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.611A pdb=" N THR D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 255 Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.968A pdb=" N VAL D 289 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.531A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.653A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.276A pdb=" N LEU D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 406 removed outlier: 3.872A pdb=" N THR D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.735A pdb=" N SER E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 46 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.532A pdb=" N PHE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.997A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 removed outlier: 3.597A pdb=" N THR E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 303 removed outlier: 4.223A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.674A pdb=" N VAL E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.559A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.742A pdb=" N GLN E 378 " --> pdb=" O GLN E 374 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.534A pdb=" N GLU E 397 " --> pdb=" O ILE E 393 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'b' and resid 9 through 23 Processing helix chain 'b' and resid 56 through 59 Processing helix chain 'c' and resid 9 through 22 removed outlier: 3.677A pdb=" N HIS c 22 " --> pdb=" O LEU c 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 23 Processing helix chain 'a' and resid 9 through 22 removed outlier: 3.707A pdb=" N HIS a 22 " --> pdb=" O LEU a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 7.793A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.634A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.634A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A 341 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 57 removed outlier: 7.540A pdb=" N TYR B 80 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N LYS B 115 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.536A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.302A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP B 265 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 207 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.882A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.624A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASP C 265 " --> pdb=" O MET C 205 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 207 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.624A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.790A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.863A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.323A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP D 265 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 207 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.381A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.374A pdb=" N ILE D 168 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.876A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU E 114 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ARG E 102 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.579A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.613A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 35 through 37 removed outlier: 6.550A pdb=" N THR b 27 " --> pdb=" O PHE b 71 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE b 71 " --> pdb=" O THR b 27 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU b 29 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 40 through 46 removed outlier: 4.072A pdb=" N ASP b 42 " --> pdb=" O VAL b 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL b 53 " --> pdb=" O ASP b 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 61 through 64 removed outlier: 6.041A pdb=" N VAL c 49 " --> pdb=" O SER c 45 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER c 45 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR c 51 " --> pdb=" O LEU c 43 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU c 43 " --> pdb=" O TYR c 51 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL c 53 " --> pdb=" O SER c 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS c 39 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR c 27 " --> pdb=" O PHE c 71 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE c 71 " --> pdb=" O THR c 27 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU c 29 " --> pdb=" O THR c 69 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE c 71 " --> pdb=" O VAL c 79 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL c 79 " --> pdb=" O PHE c 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 61 through 64 removed outlier: 3.679A pdb=" N VAL d 53 " --> pdb=" O ASP d 42 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP d 42 " --> pdb=" O VAL d 53 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU d 55 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA d 40 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR d 27 " --> pdb=" O SER d 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER d 72 " --> pdb=" O THR d 27 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE d 71 " --> pdb=" O VAL d 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 35 through 38 removed outlier: 3.593A pdb=" N ALA a 38 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU a 26 " --> pdb=" O ALA a 38 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR a 27 " --> pdb=" O PHE a 71 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE a 71 " --> pdb=" O THR a 27 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU a 29 " --> pdb=" O THR a 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 40 through 46 removed outlier: 4.369A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL a 53 " --> pdb=" O ASP a 42 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2538 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: 6.63 Time building geometry restraints manager: 7.52 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: 6505 1.34 - 1.46: 2616 1.46 - 1.57: 10096 1.57 - 1.69: 9 1.69 - 1.81: 181 Bond restraints: 19407 Sorted by residual: bond pdb=" C4 ADP B1000 " pdb=" C5 ADP B1000 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.87e-01 bond pdb=" C4 ADP C1000 " pdb=" C5 ADP C1000 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.56e-01 bond pdb=" C4 ADP D1000 " pdb=" C5 ADP D1000 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.18e-01 bond pdb=" CB THR C 365 " pdb=" CG2 THR C 365 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.18e-01 bond pdb=" CB VAL C 260 " pdb=" CG2 VAL C 260 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.98e-01 ... (remaining 19402 not shown) Histogram of bond angle deviations from ideal: 100.22 - 107.37: 625 107.37 - 114.51: 11696 114.51 - 121.66: 9541 121.66 - 128.80: 4228 128.80 - 135.94: 78 Bond angle restraints: 26168 Sorted by residual: angle pdb=" O1B ADP D1000 " pdb=" PB ADP D1000 " pdb=" O3B ADP D1000 " ideal model delta sigma weight residual 119.90 114.01 5.89 3.00e+00 1.11e-01 3.85e+00 angle pdb=" O1B ADP B1000 " pdb=" PB ADP B1000 " pdb=" O3B ADP B1000 " ideal model delta sigma weight residual 119.90 114.08 5.82 3.00e+00 1.11e-01 3.76e+00 angle pdb=" C ILE E 321 " pdb=" N ASP E 322 " pdb=" CA ASP E 322 " ideal model delta sigma weight residual 121.54 125.17 -3.63 1.91e+00 2.74e-01 3.60e+00 angle pdb=" C ASP C 265 " pdb=" N SER C 266 " pdb=" CA SER C 266 " ideal model delta sigma weight residual 121.70 125.08 -3.38 1.80e+00 3.09e-01 3.52e+00 angle pdb=" O1B ADP B1000 " pdb=" PB ADP B1000 " pdb=" O2B ADP B1000 " ideal model delta sigma weight residual 119.90 114.29 5.61 3.00e+00 1.11e-01 3.50e+00 ... (remaining 26163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.18: 11653 23.18 - 46.37: 353 46.37 - 69.55: 16 69.55 - 92.73: 2 92.73 - 115.91: 4 Dihedral angle restraints: 12028 sinusoidal: 5050 harmonic: 6978 Sorted by residual: dihedral pdb=" O1B ADP B1000 " pdb=" O3A ADP B1000 " pdb=" PB ADP B1000 " pdb=" PA ADP B1000 " ideal model delta sinusoidal sigma weight residual -60.00 -175.92 115.91 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " pdb=" PA ADP D1000 " ideal model delta sinusoidal sigma weight residual -60.00 -170.28 110.28 1 2.00e+01 2.50e-03 3.23e+01 dihedral pdb=" O1B ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PB ADP C1000 " pdb=" PA ADP C1000 " ideal model delta sinusoidal sigma weight residual -60.00 -162.91 102.90 1 2.00e+01 2.50e-03 2.94e+01 ... (remaining 12025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1709 0.025 - 0.049: 743 0.049 - 0.074: 294 0.074 - 0.098: 127 0.098 - 0.123: 119 Chirality restraints: 2992 Sorted by residual: chirality pdb=" CA PRO B 180 " pdb=" N PRO B 180 " pdb=" C PRO B 180 " pdb=" CB PRO B 180 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE E 261 " pdb=" N ILE E 261 " pdb=" C ILE E 261 " pdb=" CB ILE E 261 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE C 261 " pdb=" N ILE C 261 " pdb=" C ILE C 261 " pdb=" CB ILE C 261 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 2989 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS b 73 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO b 74 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO b 74 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO b 74 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 179 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO B 180 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 179 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 180 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.017 5.00e-02 4.00e+02 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2326 2.75 - 3.29: 19334 3.29 - 3.82: 30739 3.82 - 4.36: 38377 4.36 - 4.90: 65013 Nonbonded interactions: 155789 Sorted by model distance: nonbonded pdb=" OG1 THR E 323 " pdb=" OD2 ASP E 328 " model vdw 2.212 2.440 nonbonded pdb=" NH1 ARG E 66 " pdb=" OD2 ASP E 78 " model vdw 2.232 2.520 nonbonded pdb=" OG1 THR D 408 " pdb=" OD1 ASP D 410 " model vdw 2.235 2.440 nonbonded pdb=" NH1 ARG D 66 " pdb=" OD2 ASP D 78 " model vdw 2.240 2.520 nonbonded pdb=" OG SER D 84 " pdb=" OD1 ASP d 14 " model vdw 2.245 2.440 ... (remaining 155784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 418) selection = (chain 'C' and resid 1 through 418) selection = (chain 'D' and resid 1 through 418) selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.470 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 52.820 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 : 0.003 0.032 19407 Z= 0.192 Angle : 0.432 5.890 26168 Z= 0.206 Chirality : 0.039 0.123 2992 Planarity : 0.003 0.035 3402 Dihedral : 10.473 115.914 7506 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.40 % Allowed : 5.90 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2400 helix: 1.31 (0.17), residues: 962 sheet: 0.59 (0.27), residues: 451 loop : 0.77 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 381 HIS 0.003 0.001 HIS c 73 PHE 0.008 0.001 PHE D 89 TYR 0.005 0.001 TYR B 110 ARG 0.003 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 311 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8988 (pm20) cc_final: 0.8653 (pm20) REVERT: A 42 HIS cc_start: 0.8557 (m-70) cc_final: 0.8283 (m-70) REVERT: A 333 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8452 (tm-30) REVERT: A 415 MET cc_start: 0.8737 (tmm) cc_final: 0.8495 (tmm) REVERT: B 134 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8457 (mp0) REVERT: B 378 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8235 (mm110) REVERT: C 334 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8173 (mp0) REVERT: C 378 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8703 (mm-40) REVERT: D 244 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8409 (mm-30) REVERT: D 284 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8734 (t) REVERT: D 285 LEU cc_start: 0.9159 (mt) cc_final: 0.8930 (mp) REVERT: D 329 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8280 (mm-30) REVERT: E 42 HIS cc_start: 0.8273 (t70) cc_final: 0.7964 (t70) REVERT: E 211 GLU cc_start: 0.8606 (tp30) cc_final: 0.8295 (tp30) REVERT: E 341 MET cc_start: 0.7341 (tpt) cc_final: 0.6460 (tmm) REVERT: b 5 TYR cc_start: 0.8469 (t80) cc_final: 0.8130 (t80) REVERT: b 12 ASP cc_start: 0.8753 (m-30) cc_final: 0.8533 (m-30) REVERT: b 46 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8175 (mtm-85) REVERT: b 73 HIS cc_start: 0.8193 (t-90) cc_final: 0.7443 (t70) REVERT: b 79 VAL cc_start: 0.9003 (t) cc_final: 0.8767 (m) REVERT: b 82 SER cc_start: 0.8805 (p) cc_final: 0.8533 (p) REVERT: d 47 LYS cc_start: 0.8900 (mptp) cc_final: 0.8627 (tptp) REVERT: d 65 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8677 (mm) outliers start: 50 outliers final: 14 residues processed: 350 average time/residue: 1.4881 time to fit residues: 577.3894 Evaluate side-chains 271 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 255 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 73 HIS Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 0.0670 chunk 185 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 374 GLN A 378 GLN D 2 ASN D 8 ASN D 41 GLN D 85 GLN D 193 GLN D 241 GLN E 2 ASN E 140 HIS E 275 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 ASN d 6 GLN d 9 ASN d 21 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19407 Z= 0.167 Angle : 0.562 10.004 26168 Z= 0.279 Chirality : 0.041 0.183 2992 Planarity : 0.004 0.041 3402 Dihedral : 6.308 102.969 2678 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.59 % Allowed : 10.93 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2400 helix: 1.80 (0.17), residues: 1007 sheet: 0.72 (0.27), residues: 413 loop : 0.50 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 381 HIS 0.005 0.001 HIS E 140 PHE 0.016 0.001 PHE A 398 TYR 0.018 0.001 TYR E 197 ARG 0.008 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 272 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8971 (mmm) cc_final: 0.8583 (mmm) REVERT: A 188 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9259 (mm) REVERT: A 333 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 415 MET cc_start: 0.8704 (tmm) cc_final: 0.8495 (tmm) REVERT: B 1 MET cc_start: 0.8369 (pmm) cc_final: 0.8057 (pmm) REVERT: B 378 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8212 (mm110) REVERT: C 87 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8291 (ttp80) REVERT: D 58 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8710 (mm) REVERT: D 284 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8700 (t) REVERT: D 329 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8237 (mm-30) REVERT: E 211 GLU cc_start: 0.8439 (tp30) cc_final: 0.8189 (tp30) REVERT: E 341 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6966 (tmm) REVERT: E 388 HIS cc_start: 0.9148 (t-90) cc_final: 0.8421 (t-90) REVERT: b 25 MET cc_start: 0.8069 (tpp) cc_final: 0.7646 (tpp) REVERT: b 46 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8291 (mtm-85) REVERT: b 73 HIS cc_start: 0.7990 (t-90) cc_final: 0.7352 (t-90) REVERT: d 47 LYS cc_start: 0.8939 (mptp) cc_final: 0.8639 (tptp) REVERT: a 25 MET cc_start: 0.6140 (tmt) cc_final: 0.5894 (tpt) outliers start: 54 outliers final: 17 residues processed: 307 average time/residue: 1.3370 time to fit residues: 460.1123 Evaluate side-chains 271 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain c residue 12 ASP Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain d residue 73 HIS Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 146 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 32 GLN E 140 HIS E 193 GLN b 23 HIS d 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19407 Z= 0.316 Angle : 0.573 9.383 26168 Z= 0.281 Chirality : 0.042 0.135 2992 Planarity : 0.004 0.042 3402 Dihedral : 6.265 99.100 2673 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.36 % Allowed : 11.17 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2400 helix: 1.86 (0.17), residues: 1009 sheet: 0.59 (0.26), residues: 423 loop : 0.40 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.012 0.001 HIS A 42 PHE 0.013 0.001 PHE A 398 TYR 0.021 0.001 TYR a 51 ARG 0.008 0.000 ARG E 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 263 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9020 (mmm) cc_final: 0.8678 (mmm) REVERT: A 188 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9279 (mm) REVERT: A 333 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8531 (tm-30) REVERT: A 415 MET cc_start: 0.8709 (tmm) cc_final: 0.8492 (tmm) REVERT: B 1 MET cc_start: 0.8337 (pmm) cc_final: 0.7982 (pmm) REVERT: B 32 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8872 (mp10) REVERT: B 244 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 378 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8269 (mm110) REVERT: C 87 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8350 (ttp80) REVERT: C 193 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8560 (mp10) REVERT: C 414 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: D 58 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8776 (mm) REVERT: D 284 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8761 (t) REVERT: D 329 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8220 (mm-30) REVERT: E 211 GLU cc_start: 0.8519 (tp30) cc_final: 0.8243 (tp30) REVERT: E 244 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8282 (mm-30) REVERT: E 384 ARG cc_start: 0.9334 (tpt90) cc_final: 0.8955 (ttp80) REVERT: b 25 MET cc_start: 0.8167 (tpp) cc_final: 0.7820 (tpp) REVERT: b 46 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8209 (mtm-85) REVERT: b 73 HIS cc_start: 0.7912 (t-90) cc_final: 0.7153 (t-90) REVERT: d 46 ARG cc_start: 0.8659 (tpp80) cc_final: 0.7928 (mmt90) REVERT: d 47 LYS cc_start: 0.8967 (mptp) cc_final: 0.8512 (tptp) outliers start: 70 outliers final: 25 residues processed: 307 average time/residue: 1.3195 time to fit residues: 454.6686 Evaluate side-chains 282 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 140 HIS E 189 GLN E 193 GLN d 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19407 Z= 0.242 Angle : 0.554 10.259 26168 Z= 0.268 Chirality : 0.041 0.133 2992 Planarity : 0.003 0.045 3402 Dihedral : 6.101 96.663 2671 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.36 % Allowed : 12.56 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2400 helix: 1.94 (0.17), residues: 1009 sheet: 0.48 (0.26), residues: 423 loop : 0.35 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 381 HIS 0.004 0.001 HIS E 140 PHE 0.014 0.001 PHE A 398 TYR 0.021 0.001 TYR E 197 ARG 0.005 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 263 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9017 (mmm) cc_final: 0.8672 (mmm) REVERT: A 188 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9274 (mm) REVERT: A 329 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8043 (mp0) REVERT: A 374 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7820 (tp-100) REVERT: B 1 MET cc_start: 0.8391 (pmm) cc_final: 0.7979 (pmm) REVERT: B 32 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8815 (mp10) REVERT: B 378 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8272 (mm110) REVERT: C 58 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8961 (mm) REVERT: C 87 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8357 (ttp80) REVERT: C 193 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: C 414 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: D 58 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8782 (mm) REVERT: D 234 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8647 (mt-10) REVERT: D 329 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8166 (mm-30) REVERT: E 211 GLU cc_start: 0.8503 (tp30) cc_final: 0.8249 (tp30) REVERT: E 244 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8208 (mm-30) REVERT: E 384 ARG cc_start: 0.9330 (tpt90) cc_final: 0.8824 (ttp80) REVERT: E 416 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6840 (ttp) REVERT: b 25 MET cc_start: 0.8278 (tpp) cc_final: 0.7967 (tpp) REVERT: b 46 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8169 (mtm-85) REVERT: b 73 HIS cc_start: 0.7886 (t-90) cc_final: 0.7196 (t-90) REVERT: d 46 ARG cc_start: 0.8684 (tpp80) cc_final: 0.7992 (mmt90) REVERT: d 47 LYS cc_start: 0.8996 (mptp) cc_final: 0.8549 (tptp) outliers start: 70 outliers final: 30 residues processed: 310 average time/residue: 1.3692 time to fit residues: 474.3184 Evaluate side-chains 289 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 249 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 9 ASN Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 378 GLN E 32 GLN E 140 HIS E 193 GLN d 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19407 Z= 0.287 Angle : 0.569 10.393 26168 Z= 0.275 Chirality : 0.041 0.157 2992 Planarity : 0.004 0.046 3402 Dihedral : 6.067 95.478 2669 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.50 % Allowed : 13.33 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2400 helix: 1.92 (0.17), residues: 1013 sheet: 0.36 (0.26), residues: 423 loop : 0.35 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 381 HIS 0.004 0.001 HIS E 140 PHE 0.013 0.001 PHE A 398 TYR 0.021 0.001 TYR E 197 ARG 0.008 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 257 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7952 (p0) REVERT: A 186 MET cc_start: 0.9027 (mmm) cc_final: 0.8703 (mmm) REVERT: A 188 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9266 (mm) REVERT: A 329 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8069 (mp0) REVERT: A 374 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7858 (tp-100) REVERT: B 1 MET cc_start: 0.8401 (pmm) cc_final: 0.7983 (pmm) REVERT: B 32 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8868 (mp10) REVERT: C 58 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8963 (mm) REVERT: C 87 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8381 (ttp80) REVERT: C 193 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: C 414 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: D 58 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8796 (mm) REVERT: D 234 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8632 (mt-10) REVERT: D 329 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8139 (mm-30) REVERT: D 405 MET cc_start: 0.8721 (mtm) cc_final: 0.8420 (mtm) REVERT: E 193 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: E 211 GLU cc_start: 0.8524 (tp30) cc_final: 0.8304 (tp30) REVERT: E 244 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8203 (mm-30) REVERT: E 384 ARG cc_start: 0.9334 (tpt90) cc_final: 0.8851 (ttp80) REVERT: E 416 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6831 (ttp) REVERT: b 25 MET cc_start: 0.8282 (tpp) cc_final: 0.7983 (tpp) REVERT: b 46 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8347 (mtm-85) REVERT: b 73 HIS cc_start: 0.7822 (t-90) cc_final: 0.7147 (t-90) REVERT: d 46 ARG cc_start: 0.8704 (tpp80) cc_final: 0.8061 (mmt90) REVERT: d 47 LYS cc_start: 0.8993 (mptp) cc_final: 0.8547 (tptp) outliers start: 73 outliers final: 36 residues processed: 307 average time/residue: 1.3479 time to fit residues: 462.7628 Evaluate side-chains 290 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 242 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 9 ASN Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 0.2980 chunk 206 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 193 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19407 Z= 0.192 Angle : 0.562 10.893 26168 Z= 0.269 Chirality : 0.041 0.132 2992 Planarity : 0.003 0.047 3402 Dihedral : 5.977 94.777 2669 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.02 % Allowed : 14.38 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2400 helix: 2.05 (0.17), residues: 1005 sheet: 0.36 (0.26), residues: 423 loop : 0.34 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS d 73 PHE 0.014 0.001 PHE A 398 TYR 0.022 0.001 TYR E 197 ARG 0.008 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 255 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8031 (p0) REVERT: A 186 MET cc_start: 0.9006 (mmm) cc_final: 0.8682 (mmm) REVERT: A 188 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9271 (mm) REVERT: A 329 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8125 (mp0) REVERT: A 374 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7773 (tp-100) REVERT: B 1 MET cc_start: 0.8398 (pmm) cc_final: 0.8017 (pmm) REVERT: B 32 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8824 (mp10) REVERT: B 378 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8488 (mm110) REVERT: C 87 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8370 (ttp80) REVERT: C 193 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: C 414 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: D 58 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8809 (mm) REVERT: D 234 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8572 (mt-10) REVERT: D 329 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D 405 MET cc_start: 0.8708 (mtm) cc_final: 0.8428 (mtm) REVERT: E 21 MET cc_start: 0.8357 (mtp) cc_final: 0.8057 (ttt) REVERT: E 193 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8417 (pm20) REVERT: E 211 GLU cc_start: 0.8504 (tp30) cc_final: 0.8292 (tp30) REVERT: E 244 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8192 (mm-30) REVERT: E 384 ARG cc_start: 0.9294 (tpt90) cc_final: 0.8860 (ttp80) REVERT: E 416 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6970 (ttp) REVERT: b 25 MET cc_start: 0.8339 (tpp) cc_final: 0.8044 (tpp) REVERT: b 46 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8331 (mtm-85) REVERT: b 73 HIS cc_start: 0.7601 (t-90) cc_final: 0.6997 (t-90) REVERT: d 46 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8065 (mmt90) REVERT: d 47 LYS cc_start: 0.9015 (mptp) cc_final: 0.8583 (tptp) outliers start: 63 outliers final: 36 residues processed: 301 average time/residue: 1.3294 time to fit residues: 448.1245 Evaluate side-chains 294 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 140 HIS ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19407 Z= 0.224 Angle : 0.574 10.932 26168 Z= 0.274 Chirality : 0.041 0.156 2992 Planarity : 0.003 0.047 3402 Dihedral : 5.949 94.708 2669 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.83 % Allowed : 14.96 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2400 helix: 2.08 (0.17), residues: 1000 sheet: 0.32 (0.25), residues: 428 loop : 0.32 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 381 HIS 0.003 0.001 HIS D 140 PHE 0.014 0.001 PHE A 398 TYR 0.023 0.001 TYR E 197 ARG 0.007 0.000 ARG c 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 251 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8077 (p0) REVERT: A 186 MET cc_start: 0.9009 (mmm) cc_final: 0.8740 (mmm) REVERT: A 188 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9261 (mm) REVERT: A 329 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8246 (mp0) REVERT: A 374 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7811 (tp-100) REVERT: B 1 MET cc_start: 0.8407 (pmm) cc_final: 0.8042 (pmm) REVERT: B 32 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8822 (mp10) REVERT: B 378 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8517 (mm110) REVERT: C 58 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8967 (mm) REVERT: C 87 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8404 (ttp80) REVERT: C 193 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8538 (mp10) REVERT: C 326 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8614 (mmmm) REVERT: C 414 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: D 58 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8814 (mm) REVERT: D 234 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8584 (mt-10) REVERT: D 329 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8301 (mm-30) REVERT: D 405 MET cc_start: 0.8711 (mtm) cc_final: 0.8423 (mtm) REVERT: E 193 GLN cc_start: 0.8739 (pt0) cc_final: 0.8429 (pm20) REVERT: E 211 GLU cc_start: 0.8520 (tp30) cc_final: 0.8294 (tp30) REVERT: E 244 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8192 (mm-30) REVERT: E 380 MET cc_start: 0.8887 (mtt) cc_final: 0.8248 (tmm) REVERT: E 384 ARG cc_start: 0.9262 (tpt90) cc_final: 0.8952 (ttp80) REVERT: E 416 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6873 (ttp) REVERT: b 25 MET cc_start: 0.8337 (tpp) cc_final: 0.8013 (tpp) REVERT: b 46 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8293 (mtm-85) REVERT: b 50 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8211 (mt-10) REVERT: b 73 HIS cc_start: 0.7624 (t-90) cc_final: 0.6955 (t-90) REVERT: d 46 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8257 (mmt90) REVERT: d 47 LYS cc_start: 0.9016 (mptp) cc_final: 0.8584 (tptp) outliers start: 59 outliers final: 36 residues processed: 292 average time/residue: 1.4732 time to fit residues: 483.7033 Evaluate side-chains 286 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 239 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 12 ASP Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN E 140 HIS E 193 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19407 Z= 0.186 Angle : 0.583 11.013 26168 Z= 0.276 Chirality : 0.041 0.147 2992 Planarity : 0.003 0.047 3402 Dihedral : 5.877 94.828 2669 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.78 % Allowed : 15.29 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2400 helix: 2.12 (0.17), residues: 997 sheet: 0.36 (0.26), residues: 423 loop : 0.29 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS c 22 PHE 0.014 0.001 PHE A 398 TYR 0.024 0.001 TYR E 197 ARG 0.008 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 248 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8052 (p0) REVERT: A 186 MET cc_start: 0.8991 (mmm) cc_final: 0.8717 (mmm) REVERT: A 188 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9268 (mm) REVERT: A 374 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7788 (tp-100) REVERT: B 1 MET cc_start: 0.8407 (pmm) cc_final: 0.8058 (pmm) REVERT: B 32 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8820 (mp10) REVERT: B 378 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8484 (mm110) REVERT: C 193 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8525 (mp10) REVERT: D 234 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8539 (mt-10) REVERT: D 289 VAL cc_start: 0.8950 (t) cc_final: 0.8630 (m) REVERT: D 329 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8266 (mm-30) REVERT: D 405 MET cc_start: 0.8671 (mtm) cc_final: 0.8291 (mtm) REVERT: E 193 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: E 211 GLU cc_start: 0.8496 (tp30) cc_final: 0.8283 (tp30) REVERT: E 244 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8210 (mm-30) REVERT: E 380 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8243 (tmm) REVERT: E 384 ARG cc_start: 0.9272 (tpt90) cc_final: 0.8832 (ttp80) REVERT: E 416 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6881 (ttp) REVERT: b 25 MET cc_start: 0.8361 (tpp) cc_final: 0.8073 (tpp) REVERT: b 46 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8292 (mtm-85) REVERT: b 50 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8120 (mt-10) REVERT: b 73 HIS cc_start: 0.7517 (t-90) cc_final: 0.6861 (t-90) REVERT: d 46 ARG cc_start: 0.8720 (tpp80) cc_final: 0.8270 (mmt90) REVERT: d 47 LYS cc_start: 0.9024 (mptp) cc_final: 0.8582 (tptp) outliers start: 58 outliers final: 33 residues processed: 290 average time/residue: 1.3775 time to fit residues: 446.1989 Evaluate side-chains 278 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 5.9990 chunk 199 optimal weight: 0.0980 chunk 212 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 192 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN E 32 GLN E 140 HIS E 193 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19407 Z= 0.212 Angle : 0.595 11.342 26168 Z= 0.282 Chirality : 0.041 0.130 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.872 95.371 2669 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.30 % Allowed : 16.20 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2400 helix: 2.08 (0.17), residues: 998 sheet: 0.36 (0.26), residues: 423 loop : 0.28 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS D 140 PHE 0.014 0.001 PHE A 398 TYR 0.025 0.001 TYR E 197 ARG 0.008 0.000 ARG c 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 243 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8016 (p0) REVERT: A 186 MET cc_start: 0.8994 (mmm) cc_final: 0.8716 (mmm) REVERT: A 188 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9258 (mm) REVERT: A 374 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7790 (tp-100) REVERT: B 1 MET cc_start: 0.8413 (pmm) cc_final: 0.8051 (pmm) REVERT: B 32 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8824 (mp10) REVERT: B 378 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8481 (mm110) REVERT: C 87 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7827 (ttp80) REVERT: C 193 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: D 234 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8557 (mt-10) REVERT: D 289 VAL cc_start: 0.8956 (t) cc_final: 0.8634 (m) REVERT: D 405 MET cc_start: 0.8673 (mtm) cc_final: 0.8358 (mtm) REVERT: E 189 GLN cc_start: 0.9150 (mt0) cc_final: 0.8897 (mt0) REVERT: E 193 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: E 211 GLU cc_start: 0.8513 (tp30) cc_final: 0.8284 (tp30) REVERT: E 244 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8184 (mm-30) REVERT: E 380 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8247 (tmm) REVERT: E 384 ARG cc_start: 0.9248 (tpt90) cc_final: 0.8972 (ttp80) REVERT: E 416 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6882 (ttp) REVERT: b 25 MET cc_start: 0.8347 (tpp) cc_final: 0.8091 (tpp) REVERT: b 50 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8109 (mt-10) REVERT: b 73 HIS cc_start: 0.7430 (t-90) cc_final: 0.6773 (t-90) REVERT: d 24 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7001 (pp) REVERT: d 46 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8274 (mmt90) REVERT: d 47 LYS cc_start: 0.9028 (mptp) cc_final: 0.8582 (tptp) outliers start: 48 outliers final: 30 residues processed: 280 average time/residue: 1.3446 time to fit residues: 421.5730 Evaluate side-chains 273 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 193 GLN E 140 HIS E 193 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19407 Z= 0.235 Angle : 0.613 11.805 26168 Z= 0.290 Chirality : 0.041 0.196 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.883 96.445 2669 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.40 % Allowed : 16.01 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2400 helix: 2.05 (0.17), residues: 998 sheet: 0.25 (0.26), residues: 431 loop : 0.28 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS D 140 PHE 0.013 0.001 PHE A 398 TYR 0.026 0.001 TYR E 197 ARG 0.008 0.000 ARG c 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 234 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8050 (p0) REVERT: A 21 MET cc_start: 0.6272 (ppp) cc_final: 0.5975 (pmm) REVERT: A 186 MET cc_start: 0.8996 (mmm) cc_final: 0.8717 (mmm) REVERT: A 188 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9263 (mm) REVERT: A 374 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7808 (tp-100) REVERT: B 1 MET cc_start: 0.8424 (pmm) cc_final: 0.8039 (pmm) REVERT: B 32 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8812 (mp10) REVERT: C 87 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8311 (mtm110) REVERT: C 193 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8529 (mp10) REVERT: D 234 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: D 285 LEU cc_start: 0.9052 (mt) cc_final: 0.8728 (mp) REVERT: D 289 VAL cc_start: 0.8956 (t) cc_final: 0.8456 (m) REVERT: D 405 MET cc_start: 0.8678 (mtm) cc_final: 0.8377 (mtm) REVERT: E 193 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: E 211 GLU cc_start: 0.8510 (tp30) cc_final: 0.8291 (tp30) REVERT: E 244 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8207 (mm-30) REVERT: E 341 MET cc_start: 0.7099 (mpm) cc_final: 0.6412 (tmm) REVERT: E 380 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8253 (tmm) REVERT: E 384 ARG cc_start: 0.9257 (tpt90) cc_final: 0.9030 (ttp80) REVERT: E 416 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6754 (ttp) REVERT: b 25 MET cc_start: 0.8329 (tpp) cc_final: 0.8048 (tpp) REVERT: b 50 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8096 (mt-10) REVERT: b 73 HIS cc_start: 0.7418 (t-90) cc_final: 0.6749 (t-90) REVERT: d 24 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6975 (pp) REVERT: d 46 ARG cc_start: 0.8725 (tpp80) cc_final: 0.8207 (mmt90) REVERT: d 47 LYS cc_start: 0.9041 (mptp) cc_final: 0.8590 (tptp) outliers start: 50 outliers final: 34 residues processed: 272 average time/residue: 1.3317 time to fit residues: 406.0507 Evaluate side-chains 279 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 234 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 78 optimal weight: 0.0070 chunk 193 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 10 optimal weight: 0.0370 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN E 32 GLN E 140 HIS E 193 GLN ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 9 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.099699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069031 restraints weight = 42531.471| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.74 r_work: 0.2890 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19407 Z= 0.197 Angle : 0.605 11.828 26168 Z= 0.285 Chirality : 0.041 0.151 2992 Planarity : 0.003 0.047 3402 Dihedral : 5.848 97.484 2669 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.21 % Allowed : 16.35 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2400 helix: 2.01 (0.17), residues: 1006 sheet: 0.28 (0.26), residues: 431 loop : 0.32 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.004 0.001 HIS E 42 PHE 0.014 0.001 PHE A 398 TYR 0.026 0.001 TYR E 197 ARG 0.013 0.000 ARG A 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7579.36 seconds wall clock time: 132 minutes 59.27 seconds (7979.27 seconds total)