Starting phenix.real_space_refine on Sat Mar 7 01:09:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nsu_12577/03_2026/7nsu_12577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nsu_12577/03_2026/7nsu_12577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nsu_12577/03_2026/7nsu_12577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nsu_12577/03_2026/7nsu_12577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nsu_12577/03_2026/7nsu_12577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nsu_12577/03_2026/7nsu_12577.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.033 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 S 27 5.16 5 C 11613 2.51 5 N 3196 2.21 5 O 3707 1.98 5 H 17527 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36070 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5071 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain: "B" Number of atoms: 5071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5071 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain: "C" Number of atoms: 5070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5070 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain: "D" Number of atoms: 6003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 6003 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 24, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 6000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 5856 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 26, 'TRANS': 367} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 5856 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 26, 'TRANS': 367} Chain breaks: 1 bond proxies already assigned to first conformer: 5772 Chain: "F" Number of atoms: 8855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 8855 Classifications: {'peptide': 576} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 557} Chain breaks: 1 Time building chain proxies: 6.32, per 1000 atoms: 0.18 Number of scatterers: 36070 At special positions: 0 Unit cell: (189.507, 100.512, 145.533, 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 27 16.00 O 3707 8.00 N 3196 7.00 C 11613 6.00 H 17527 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS E 201 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 21 sheets defined 14.7% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 103 through 110 removed outlier: 3.533A pdb=" N ASP A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.523A pdb=" N ASP B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'C' and resid 103 through 110 removed outlier: 3.630A pdb=" N ASP C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 197 through 203 Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.607A pdb=" N LYS D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 149 removed outlier: 3.916A pdb=" N LYS D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.853A pdb=" N GLY D 280 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 313 removed outlier: 3.922A pdb=" N ALA D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 377 removed outlier: 3.813A pdb=" N GLU D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 382 removed outlier: 4.263A pdb=" N HIS D 381 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 446 removed outlier: 3.695A pdb=" N MET D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN D 392 " --> pdb=" O HIS D 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 65 Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.739A pdb=" N TRP E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 140 through 158 Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 31 through 38 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 71 No H-bonds generated for 'chain 'F' and resid 70 through 71' Processing helix chain 'F' and resid 72 through 76 removed outlier: 3.654A pdb=" N VAL F 76 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 92 removed outlier: 4.625A pdb=" N SER F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 104 removed outlier: 3.692A pdb=" N LEU F 103 " --> pdb=" O PRO F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 Processing helix chain 'F' and resid 325 through 329 removed outlier: 3.519A pdb=" N VAL F 329 " --> pdb=" O THR F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 6 current: chain 'A' and resid 55 through 66 removed outlier: 6.444A pdb=" N ASN A 64 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N THR A 81 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N ARG A 82 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A 102 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN A 101 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY A 134 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 273 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 297 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR A 275 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE A 295 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS A 277 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN A 293 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS A 279 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 291 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS A 281 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 289 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 6 current: chain 'B' and resid 55 through 66 removed outlier: 6.440A pdb=" N ASN B 64 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR B 81 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N ARG B 82 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR B 102 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN B 101 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLY B 134 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 292 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 280 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP B 290 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP B 282 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 288 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 6 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 6 current: chain 'C' and resid 55 through 66 removed outlier: 6.538A pdb=" N ASN C 64 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR C 81 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 12.536A pdb=" N ARG C 82 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR C 102 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN C 101 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLY C 134 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 292 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA C 280 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASP C 290 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP C 282 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'D' and resid 94 through 96 removed outlier: 19.821A pdb=" N THR D 268 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 13.991A pdb=" N ASP D 270 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N SER D 206 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL D 272 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG D 274 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 210 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY D 202 " --> pdb=" O ASN D 183 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N ASN D 183 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ASN D 181 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER D 206 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR D 179 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 removed outlier: 19.821A pdb=" N THR D 268 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 13.991A pdb=" N ASP D 270 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N SER D 206 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL D 272 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG D 274 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 210 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLN D 195 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER D 139 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE D 197 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 201 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE D 133 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 104 removed outlier: 6.458A pdb=" N LEU D 103 " --> pdb=" O ASN D 232 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER D 234 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 68 through 70 removed outlier: 9.130A pdb=" N VAL E 100 " --> pdb=" O PRO E 36 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY E 38 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N GLY E 102 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 130 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP E 120 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL E 128 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 193 through 198 removed outlier: 5.195A pdb=" N VAL E 194 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL E 184 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG E 166 " --> pdb=" O TRP E 426 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TRP E 426 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA E 168 " --> pdb=" O PRO E 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 206 through 207 removed outlier: 3.546A pdb=" N ALA E 206 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 226 " --> pdb=" O VAL E 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 251 removed outlier: 5.322A pdb=" N ALA E 248 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA E 261 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 290 through 295 removed outlier: 5.548A pdb=" N GLU E 292 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR E 305 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 333 through 339 removed outlier: 4.674A pdb=" N ALA E 337 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL E 347 " --> pdb=" O ALA E 337 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL E 339 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE E 345 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E 355 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 378 through 382 removed outlier: 5.407A pdb=" N THR E 379 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER E 392 " --> pdb=" O THR E 379 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AB9, first strand: chain 'F' and resid 26 through 30 Processing sheet with id=AC1, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AC2, first strand: chain 'F' and resid 137 through 145 removed outlier: 8.805A pdb=" N THR F 370 " --> pdb=" O TYR F 393 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N TYR F 393 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN F 372 " --> pdb=" O THR F 391 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR F 391 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER F 374 " --> pdb=" O TYR F 389 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR F 389 " --> pdb=" O SER F 374 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLY F 376 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA F 387 " --> pdb=" O GLY F 376 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLU F 378 " --> pdb=" O PHE F 385 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE F 385 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL F 429 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE F 470 " --> pdb=" O VAL F 429 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP F 431 " --> pdb=" O ALA F 468 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA F 468 " --> pdb=" O TRP F 431 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE F 433 " --> pdb=" O ALA F 466 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA F 466 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY F 435 " --> pdb=" O VAL F 464 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 464 " --> pdb=" O GLY F 435 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG F 437 " --> pdb=" O LYS F 462 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS F 462 " --> pdb=" O ARG F 437 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP F 439 " --> pdb=" O ARG F 460 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG F 460 " --> pdb=" O ASP F 439 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER F 441 " --> pdb=" O LYS F 458 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS F 458 " --> pdb=" O SER F 441 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU F 443 " --> pdb=" O GLU F 456 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 527 through 529 952 hydrogen bonds defined for protein. 2628 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: 8.99 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 17527 1.04 - 1.25: 3241 1.25 - 1.46: 7465 1.46 - 1.67: 8202 1.67 - 1.88: 52 Bond restraints: 36487 Sorted by residual: bond pdb=" CB CYS D 33 " pdb=" SG CYS D 33 " ideal model delta sigma weight residual 1.808 1.877 -0.069 3.30e-02 9.18e+02 4.39e+00 bond pdb=" CB PRO D 383 " pdb=" CG PRO D 383 " ideal model delta sigma weight residual 1.492 1.404 0.088 5.00e-02 4.00e+02 3.12e+00 bond pdb=" CB TYR F 405 " pdb=" CG TYR F 405 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.20e-02 2.07e+03 1.71e+00 bond pdb=" CA SER C 95 " pdb=" CB SER C 95 " ideal model delta sigma weight residual 1.534 1.512 0.021 1.78e-02 3.16e+03 1.45e+00 bond pdb=" CA TYR C 58 " pdb=" CB TYR C 58 " ideal model delta sigma weight residual 1.535 1.513 0.022 2.09e-02 2.29e+03 1.12e+00 ... (remaining 36482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 64505 1.90 - 3.79: 758 3.79 - 5.69: 71 5.69 - 7.58: 8 7.58 - 9.48: 3 Bond angle restraints: 65345 Sorted by residual: angle pdb=" C SER D 17 " pdb=" N GLY D 18 " pdb=" CA GLY D 18 " ideal model delta sigma weight residual 119.92 124.13 -4.21 9.60e-01 1.09e+00 1.92e+01 angle pdb=" N CYS E 201 " pdb=" CA CYS E 201 " pdb=" C CYS E 201 " ideal model delta sigma weight residual 110.42 115.79 -5.37 1.46e+00 4.69e-01 1.35e+01 angle pdb=" N GLY D 32 " pdb=" CA GLY D 32 " pdb=" C GLY D 32 " ideal model delta sigma weight residual 113.18 104.53 8.65 2.37e+00 1.78e-01 1.33e+01 angle pdb=" N ASP F 162 " pdb=" CA ASP F 162 " pdb=" C ASP F 162 " ideal model delta sigma weight residual 114.12 109.25 4.87 1.39e+00 5.18e-01 1.23e+01 angle pdb=" C SER D 30 " pdb=" N GLY D 31 " pdb=" CA GLY D 31 " ideal model delta sigma weight residual 121.60 131.08 -9.48 2.86e+00 1.22e-01 1.10e+01 ... (remaining 65340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15621 17.98 - 35.96: 1253 35.96 - 53.94: 401 53.94 - 71.93: 120 71.93 - 89.91: 14 Dihedral angle restraints: 17409 sinusoidal: 9215 harmonic: 8194 Sorted by residual: dihedral pdb=" CA LEU E 302 " pdb=" C LEU E 302 " pdb=" N ALA E 303 " pdb=" CA ALA E 303 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA MET E 203 " pdb=" C MET E 203 " pdb=" N SER E 204 " pdb=" CA SER E 204 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP A 127 " pdb=" C ASP A 127 " pdb=" N PHE A 128 " pdb=" CA PHE A 128 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 17406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1764 0.036 - 0.073: 625 0.073 - 0.109: 189 0.109 - 0.146: 115 0.146 - 0.182: 4 Chirality restraints: 2697 Sorted by residual: chirality pdb=" CA ILE E 159 " pdb=" N ILE E 159 " pdb=" C ILE E 159 " pdb=" CB ILE E 159 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA VAL D 29 " pdb=" N VAL D 29 " pdb=" C VAL D 29 " pdb=" CB VAL D 29 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE B 187 " pdb=" N ILE B 187 " pdb=" C ILE B 187 " pdb=" CB ILE B 187 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 2694 not shown) Planarity restraints: 5790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 440 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLU D 440 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU D 440 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS D 441 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 153 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C PHE E 153 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE E 153 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU E 154 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 324 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C TYR D 324 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR D 324 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D 325 " 0.019 2.00e-02 2.50e+03 ... (remaining 5787 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 772 2.07 - 2.70: 58582 2.70 - 3.33: 104557 3.33 - 3.97: 136206 3.97 - 4.60: 210956 Nonbonded interactions: 511073 Sorted by model distance: nonbonded pdb=" O HIS F 75 " pdb=" H GLY F 124 " model vdw 1.434 2.450 nonbonded pdb=" OD2 ASP F 528 " pdb=" H TYR F 577 " model vdw 1.483 2.450 nonbonded pdb="HE22 GLN F 364 " pdb=" O PRO F 408 " model vdw 1.485 2.450 nonbonded pdb=" O VAL D 29 " pdb="HE22 GLN E 172 " model vdw 1.489 2.450 nonbonded pdb=" OE1 GLU D 167 " pdb=" H GLU D 167 " model vdw 1.523 2.450 ... (remaining 511068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 89 or (resid 90 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2)) or resid 91 through 340)) selection = (chain 'B' and (resid 1 through 89 or (resid 90 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2)) or resid 91 through 340)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.210 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 32.940 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5030 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 0.088 18961 Z= 0.172 Angle : 0.700 9.478 25746 Z= 0.402 Chirality : 0.046 0.182 2697 Planarity : 0.005 0.054 3458 Dihedral : 14.513 89.907 6748 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.85 % Favored : 95.02 % Rotamer: Outliers : 3.66 % Allowed : 7.07 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2401 helix: -2.33 (0.25), residues: 248 sheet: -0.58 (0.15), residues: 1069 loop : -1.52 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 237 TYR 0.025 0.002 TYR D 324 PHE 0.017 0.002 PHE E 219 TRP 0.023 0.002 TRP E 207 HIS 0.005 0.001 HIS D 388 Details of bonding type rmsd covalent geometry : bond 0.00330 (18960) covalent geometry : angle 0.69802 (25744) SS BOND : bond 0.01808 ( 1) SS BOND : angle 6.39164 ( 2) hydrogen bonds : bond 0.12595 ( 936) hydrogen bonds : angle 6.94552 ( 2628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 560 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 492 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8140 (pttt) cc_final: 0.7872 (pttt) REVERT: A 38 MET cc_start: 0.8041 (mmt) cc_final: 0.7527 (mmt) REVERT: A 40 TYR cc_start: 0.6689 (p90) cc_final: 0.6484 (p90) REVERT: A 65 PHE cc_start: 0.7071 (m-80) cc_final: 0.6354 (m-80) REVERT: A 90 TYR cc_start: 0.7624 (t80) cc_final: 0.6823 (t80) REVERT: A 92 ASP cc_start: 0.8514 (p0) cc_final: 0.8066 (p0) REVERT: A 160 LYS cc_start: 0.8270 (ttmt) cc_final: 0.8039 (ttpp) REVERT: A 243 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8710 (mmtp) REVERT: A 258 LEU cc_start: 0.7001 (mm) cc_final: 0.6768 (mm) REVERT: A 267 PHE cc_start: 0.7909 (p90) cc_final: 0.7582 (p90) REVERT: A 281 LYS cc_start: 0.8635 (mttp) cc_final: 0.8228 (mttp) REVERT: A 310 TYR cc_start: 0.7545 (p90) cc_final: 0.7343 (p90) REVERT: A 337 VAL cc_start: 0.7296 (t) cc_final: 0.6305 (t) REVERT: B 66 GLN cc_start: 0.6955 (mm110) cc_final: 0.6379 (mm110) REVERT: B 100 ARG cc_start: 0.7437 (ttt90) cc_final: 0.7065 (ttt90) REVERT: B 109 LEU cc_start: 0.7827 (mt) cc_final: 0.7624 (mt) REVERT: B 139 TYR cc_start: 0.7002 (t80) cc_final: 0.6702 (t80) REVERT: B 177 SER cc_start: 0.7123 (t) cc_final: 0.6833 (p) REVERT: B 201 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8253 (mt-10) REVERT: B 219 LYS cc_start: 0.7352 (pttt) cc_final: 0.7082 (pttt) REVERT: B 233 GLU cc_start: 0.5234 (tt0) cc_final: 0.4576 (tp30) REVERT: B 241 THR cc_start: 0.6694 (p) cc_final: 0.6462 (p) REVERT: B 262 GLN cc_start: 0.7256 (mt0) cc_final: 0.6887 (mt0) REVERT: B 263 TYR cc_start: 0.8074 (t80) cc_final: 0.7415 (t80) REVERT: B 289 VAL cc_start: 0.4976 (p) cc_final: 0.3982 (m) REVERT: B 295 PHE cc_start: 0.6886 (m-10) cc_final: 0.6653 (m-10) REVERT: C 38 MET cc_start: 0.7816 (mmt) cc_final: 0.7236 (mmt) REVERT: C 55 LEU cc_start: 0.8467 (tp) cc_final: 0.8003 (tp) REVERT: C 85 PHE cc_start: 0.6967 (p90) cc_final: 0.6445 (p90) REVERT: C 207 ASN cc_start: 0.7534 (t0) cc_final: 0.7305 (m110) REVERT: C 316 ASN cc_start: 0.7519 (t0) cc_final: 0.7272 (t0) REVERT: D 284 VAL cc_start: -0.0338 (OUTLIER) cc_final: -0.0573 (t) REVERT: E 142 ARG cc_start: 0.4112 (mtp85) cc_final: 0.3863 (mtp85) REVERT: F 150 GLN cc_start: 0.5491 (pt0) cc_final: 0.4831 (pt0) REVERT: F 152 TYR cc_start: 0.8147 (m-80) cc_final: 0.7465 (m-10) REVERT: F 153 ASP cc_start: 0.6796 (t0) cc_final: 0.6584 (t0) REVERT: F 157 GLN cc_start: 0.5352 (OUTLIER) cc_final: 0.4809 (pt0) REVERT: F 176 HIS cc_start: 0.5126 (m90) cc_final: 0.4780 (m90) REVERT: F 261 ILE cc_start: 0.4603 (pt) cc_final: 0.4146 (tp) REVERT: F 262 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6817 (mmtm) REVERT: F 266 ILE cc_start: 0.7929 (mt) cc_final: 0.6914 (mt) REVERT: F 293 MET cc_start: 0.5196 (tmm) cc_final: 0.4979 (mmm) REVERT: F 305 ILE cc_start: 0.7062 (mm) cc_final: 0.6843 (mt) REVERT: F 487 ARG cc_start: 0.6005 (mtt-85) cc_final: 0.5725 (mtm110) REVERT: F 513 ASP cc_start: 0.6283 (m-30) cc_final: 0.6055 (t0) REVERT: F 548 ASP cc_start: 0.6480 (m-30) cc_final: 0.5791 (t0) REVERT: F 565 ILE cc_start: 0.3653 (mp) cc_final: 0.3295 (mp) outliers start: 68 outliers final: 36 residues processed: 547 average time/residue: 0.3421 time to fit residues: 272.3626 Evaluate side-chains 482 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 443 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN E 334 ASN ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN F 368 HIS ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.222084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.169861 restraints weight = 185677.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.180959 restraints weight = 95075.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.187896 restraints weight = 52935.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.192013 restraints weight = 31866.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.194577 restraints weight = 20913.635| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4487 r_free = 0.4487 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4486 r_free = 0.4486 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| r_final: 0.4486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 18961 Z= 0.380 Angle : 0.823 11.290 25746 Z= 0.464 Chirality : 0.049 0.178 2697 Planarity : 0.007 0.124 3458 Dihedral : 5.729 27.259 2678 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 0.31 % Allowed : 3.25 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.16), residues: 2401 helix: -0.64 (0.28), residues: 255 sheet: -0.55 (0.15), residues: 1112 loop : -1.24 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 274 TYR 0.034 0.003 TYR F 383 PHE 0.028 0.003 PHE C 23 TRP 0.025 0.003 TRP E 426 HIS 0.021 0.004 HIS D 315 Details of bonding type rmsd covalent geometry : bond 0.00735 (18960) covalent geometry : angle 0.82231 (25744) SS BOND : bond 0.04851 ( 1) SS BOND : angle 2.91722 ( 2) hydrogen bonds : bond 0.05681 ( 936) hydrogen bonds : angle 6.74012 ( 2628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 462 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 458 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TYR cc_start: 0.7540 (p90) cc_final: 0.6910 (p90) REVERT: A 38 MET cc_start: 0.8385 (mmt) cc_final: 0.7618 (mmt) REVERT: A 46 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7581 (mtmt) REVERT: A 65 PHE cc_start: 0.7080 (m-80) cc_final: 0.6664 (m-80) REVERT: A 90 TYR cc_start: 0.7504 (t80) cc_final: 0.6857 (t80) REVERT: A 92 ASP cc_start: 0.8435 (p0) cc_final: 0.7972 (p0) REVERT: A 128 PHE cc_start: 0.7668 (m-80) cc_final: 0.6845 (m-80) REVERT: A 129 PHE cc_start: 0.7088 (m-80) cc_final: 0.6599 (m-80) REVERT: A 160 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8682 (ttpp) REVERT: A 267 PHE cc_start: 0.8509 (p90) cc_final: 0.8223 (p90) REVERT: A 281 LYS cc_start: 0.8758 (mttp) cc_final: 0.8278 (mttp) REVERT: A 307 MET cc_start: 0.7774 (tpp) cc_final: 0.7433 (tpp) REVERT: A 310 TYR cc_start: 0.7966 (p90) cc_final: 0.7587 (p90) REVERT: A 321 ASP cc_start: 0.7025 (m-30) cc_final: 0.6816 (m-30) REVERT: B 4 TYR cc_start: 0.7535 (t80) cc_final: 0.7178 (t80) REVERT: B 66 GLN cc_start: 0.7130 (mm110) cc_final: 0.6604 (mm110) REVERT: B 97 ASP cc_start: 0.8356 (p0) cc_final: 0.8128 (p0) REVERT: B 109 LEU cc_start: 0.8268 (mt) cc_final: 0.8055 (mt) REVERT: B 124 TYR cc_start: 0.7673 (m-80) cc_final: 0.7284 (m-80) REVERT: B 156 GLN cc_start: 0.7568 (tt0) cc_final: 0.7125 (tt0) REVERT: B 164 ASP cc_start: 0.8219 (p0) cc_final: 0.7917 (p0) REVERT: B 177 SER cc_start: 0.7282 (t) cc_final: 0.6663 (m) REVERT: B 183 GLU cc_start: 0.8270 (tt0) cc_final: 0.7232 (mt-10) REVERT: B 191 TYR cc_start: 0.7324 (t80) cc_final: 0.6723 (t80) REVERT: B 201 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 224 ASN cc_start: 0.9016 (m-40) cc_final: 0.8609 (m-40) REVERT: B 262 GLN cc_start: 0.7554 (mt0) cc_final: 0.7189 (mt0) REVERT: B 263 TYR cc_start: 0.8374 (t80) cc_final: 0.7850 (t80) REVERT: B 305 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8089 (ptpp) REVERT: C 38 MET cc_start: 0.8153 (mmt) cc_final: 0.7625 (mmt) REVERT: C 49 THR cc_start: 0.8240 (t) cc_final: 0.7928 (t) REVERT: C 50 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8336 (tp-100) REVERT: C 68 ASN cc_start: 0.8108 (p0) cc_final: 0.7788 (p0) REVERT: C 79 ASN cc_start: 0.8110 (m-40) cc_final: 0.7880 (m110) REVERT: C 85 PHE cc_start: 0.6981 (p90) cc_final: 0.6388 (p90) REVERT: C 114 MET cc_start: 0.7032 (mmm) cc_final: 0.6220 (mtm) REVERT: C 160 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8523 (ttmt) REVERT: C 207 ASN cc_start: 0.7994 (t0) cc_final: 0.7660 (m110) REVERT: C 316 ASN cc_start: 0.7746 (t0) cc_final: 0.7483 (t0) REVERT: D 205 MET cc_start: 0.1921 (mtm) cc_final: 0.1595 (mtm) REVERT: E 142 ARG cc_start: 0.4946 (mtp85) cc_final: 0.4624 (mtp85) REVERT: F 261 ILE cc_start: 0.5394 (pt) cc_final: 0.4941 (tp) REVERT: F 263 SER cc_start: 0.7611 (t) cc_final: 0.7386 (m) REVERT: F 345 LEU cc_start: 0.7169 (tt) cc_final: 0.5979 (pp) REVERT: F 384 ARG cc_start: 0.2788 (OUTLIER) cc_final: 0.2341 (ptp-170) REVERT: F 487 ARG cc_start: 0.6590 (mtt-85) cc_final: 0.6167 (mtt90) REVERT: F 513 ASP cc_start: 0.7177 (m-30) cc_final: 0.6801 (t0) REVERT: F 548 ASP cc_start: 0.6779 (m-30) cc_final: 0.5952 (t0) REVERT: F 565 ILE cc_start: 0.3860 (mp) cc_final: 0.2879 (mp) REVERT: F 592 TYR cc_start: 0.6927 (t80) cc_final: 0.6435 (t80) outliers start: 4 outliers final: 2 residues processed: 461 average time/residue: 0.3226 time to fit residues: 218.8198 Evaluate side-chains 435 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 21 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN E 87 GLN E 334 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 GLN F 521 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.226347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.175674 restraints weight = 165892.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.186085 restraints weight = 86439.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.192849 restraints weight = 49117.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.196966 restraints weight = 30263.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.199198 restraints weight = 19738.785| |-----------------------------------------------------------------------------| r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4537 r_free = 0.4537 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4537 r_free = 0.4537 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.4537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18961 Z= 0.217 Angle : 0.629 8.821 25746 Z= 0.353 Chirality : 0.045 0.187 2697 Planarity : 0.005 0.092 3458 Dihedral : 5.314 29.657 2678 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.10 % Allowed : 1.52 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2401 helix: 0.33 (0.30), residues: 253 sheet: -0.46 (0.15), residues: 1114 loop : -1.04 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 562 TYR 0.031 0.002 TYR C 313 PHE 0.018 0.002 PHE C 244 TRP 0.015 0.002 TRP F 418 HIS 0.010 0.002 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00420 (18960) covalent geometry : angle 0.62900 (25744) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.80469 ( 2) hydrogen bonds : bond 0.04453 ( 936) hydrogen bonds : angle 6.33013 ( 2628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8310 (pttt) cc_final: 0.8106 (pttt) REVERT: A 40 TYR cc_start: 0.6321 (p90) cc_final: 0.6018 (p90) REVERT: A 65 PHE cc_start: 0.7144 (m-10) cc_final: 0.6772 (m-10) REVERT: A 90 TYR cc_start: 0.7460 (t80) cc_final: 0.6764 (t80) REVERT: A 92 ASP cc_start: 0.8323 (p0) cc_final: 0.7836 (p0) REVERT: A 129 PHE cc_start: 0.6909 (m-80) cc_final: 0.6423 (m-80) REVERT: A 160 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8521 (ttpp) REVERT: A 267 PHE cc_start: 0.8475 (p90) cc_final: 0.8195 (p90) REVERT: A 281 LYS cc_start: 0.8730 (mttp) cc_final: 0.8230 (mttp) REVERT: A 307 MET cc_start: 0.7752 (tpp) cc_final: 0.7434 (tpp) REVERT: A 310 TYR cc_start: 0.7921 (p90) cc_final: 0.7289 (p90) REVERT: A 321 ASP cc_start: 0.6856 (m-30) cc_final: 0.6636 (m-30) REVERT: B 4 TYR cc_start: 0.7410 (t80) cc_final: 0.6778 (t80) REVERT: B 64 ASN cc_start: 0.7395 (t0) cc_final: 0.7007 (t0) REVERT: B 79 ASN cc_start: 0.7949 (m-40) cc_final: 0.7721 (m-40) REVERT: B 97 ASP cc_start: 0.8246 (p0) cc_final: 0.8041 (p0) REVERT: B 124 TYR cc_start: 0.7582 (m-80) cc_final: 0.7261 (m-80) REVERT: B 164 ASP cc_start: 0.8288 (p0) cc_final: 0.7876 (p0) REVERT: B 183 GLU cc_start: 0.8155 (tt0) cc_final: 0.7144 (mt-10) REVERT: B 201 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 219 LYS cc_start: 0.7502 (pttt) cc_final: 0.7040 (pttt) REVERT: B 224 ASN cc_start: 0.8887 (m-40) cc_final: 0.8458 (m-40) REVERT: B 262 GLN cc_start: 0.7581 (mt0) cc_final: 0.7209 (mt0) REVERT: B 263 TYR cc_start: 0.8209 (t80) cc_final: 0.7712 (t80) REVERT: B 295 PHE cc_start: 0.7166 (m-10) cc_final: 0.6892 (m-10) REVERT: B 305 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8013 (ptpp) REVERT: C 38 MET cc_start: 0.8114 (mmt) cc_final: 0.7542 (mmt) REVERT: C 49 THR cc_start: 0.8164 (t) cc_final: 0.7910 (t) REVERT: C 85 PHE cc_start: 0.6808 (p90) cc_final: 0.6331 (p90) REVERT: C 114 MET cc_start: 0.6989 (mmm) cc_final: 0.6429 (mtm) REVERT: C 160 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8426 (ttmt) REVERT: C 207 ASN cc_start: 0.7951 (t0) cc_final: 0.7621 (m110) REVERT: C 260 VAL cc_start: 0.7592 (p) cc_final: 0.7119 (p) REVERT: C 303 PHE cc_start: 0.7274 (m-80) cc_final: 0.6888 (m-80) REVERT: C 316 ASN cc_start: 0.7703 (t0) cc_final: 0.7499 (t0) REVERT: D 205 MET cc_start: 0.1801 (mtm) cc_final: 0.1514 (mtm) REVERT: E 142 ARG cc_start: 0.5275 (mtp85) cc_final: 0.4892 (mtp85) REVERT: F 135 GLU cc_start: 0.7928 (mp0) cc_final: 0.7492 (mp0) REVERT: F 166 VAL cc_start: 0.6559 (m) cc_final: 0.6260 (p) REVERT: F 264 GLN cc_start: 0.7338 (pp30) cc_final: 0.6818 (pp30) REVERT: F 266 ILE cc_start: 0.7538 (mt) cc_final: 0.7309 (mt) REVERT: F 345 LEU cc_start: 0.7289 (tt) cc_final: 0.6136 (pp) REVERT: F 487 ARG cc_start: 0.6392 (mtt-85) cc_final: 0.6142 (mtt90) REVERT: F 512 TYR cc_start: 0.4286 (m-10) cc_final: 0.4031 (m-10) REVERT: F 513 ASP cc_start: 0.7028 (m-30) cc_final: 0.6571 (t0) REVERT: F 548 ASP cc_start: 0.6411 (m-30) cc_final: 0.5660 (t0) REVERT: F 565 ILE cc_start: 0.3630 (mp) cc_final: 0.2912 (mp) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.3252 time to fit residues: 216.4465 Evaluate side-chains 431 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 103 optimal weight: 0.0170 chunk 200 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 110 optimal weight: 50.0000 chunk 189 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 overall best weight: 1.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS E 334 ASN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.229297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.178191 restraints weight = 191192.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.190176 restraints weight = 96452.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.196341 restraints weight = 54786.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.200954 restraints weight = 31486.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.204090 restraints weight = 19976.896| |-----------------------------------------------------------------------------| r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4561 r_free = 0.4561 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4561 r_free = 0.4561 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.4561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5268 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18961 Z= 0.137 Angle : 0.550 7.326 25746 Z= 0.305 Chirality : 0.045 0.163 2697 Planarity : 0.005 0.135 3458 Dihedral : 4.980 27.949 2678 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.21 % Allowed : 1.15 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2401 helix: 1.43 (0.33), residues: 234 sheet: -0.41 (0.15), residues: 1112 loop : -0.82 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 526 TYR 0.021 0.002 TYR F 275 PHE 0.013 0.001 PHE C 244 TRP 0.015 0.002 TRP F 418 HIS 0.006 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00274 (18960) covalent geometry : angle 0.54943 (25744) SS BOND : bond 0.01161 ( 1) SS BOND : angle 1.17890 ( 2) hydrogen bonds : bond 0.03597 ( 936) hydrogen bonds : angle 5.89856 ( 2628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 451 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8244 (tp) cc_final: 0.7960 (tp) REVERT: A 20 LEU cc_start: 0.7144 (tp) cc_final: 0.6877 (tp) REVERT: A 38 MET cc_start: 0.8114 (mmt) cc_final: 0.7462 (mmt) REVERT: A 40 TYR cc_start: 0.6357 (p90) cc_final: 0.6078 (p90) REVERT: A 85 PHE cc_start: 0.7227 (p90) cc_final: 0.6915 (p90) REVERT: A 90 TYR cc_start: 0.7195 (t80) cc_final: 0.6671 (t80) REVERT: A 92 ASP cc_start: 0.8287 (p0) cc_final: 0.7831 (p0) REVERT: A 115 LEU cc_start: 0.8440 (mm) cc_final: 0.8137 (mm) REVERT: A 129 PHE cc_start: 0.6767 (m-80) cc_final: 0.6311 (m-80) REVERT: A 160 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8408 (ttpp) REVERT: A 161 ASN cc_start: 0.8559 (t0) cc_final: 0.8117 (t0) REVERT: A 267 PHE cc_start: 0.8323 (p90) cc_final: 0.7942 (p90) REVERT: A 281 LYS cc_start: 0.8627 (mttp) cc_final: 0.8206 (mttp) REVERT: A 307 MET cc_start: 0.7734 (tpp) cc_final: 0.7423 (tpp) REVERT: A 310 TYR cc_start: 0.7697 (p90) cc_final: 0.7150 (p90) REVERT: B 4 TYR cc_start: 0.7407 (t80) cc_final: 0.6706 (t80) REVERT: B 6 LYS cc_start: 0.8048 (tttm) cc_final: 0.7728 (tttp) REVERT: B 64 ASN cc_start: 0.6774 (t0) cc_final: 0.6399 (t0) REVERT: B 97 ASP cc_start: 0.8051 (p0) cc_final: 0.7780 (p0) REVERT: B 104 VAL cc_start: 0.8569 (p) cc_final: 0.8356 (p) REVERT: B 109 LEU cc_start: 0.8008 (mt) cc_final: 0.7746 (mt) REVERT: B 124 TYR cc_start: 0.7575 (m-80) cc_final: 0.7327 (m-80) REVERT: B 164 ASP cc_start: 0.8307 (p0) cc_final: 0.7822 (p0) REVERT: B 183 GLU cc_start: 0.8132 (tt0) cc_final: 0.7120 (mt-10) REVERT: B 201 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8157 (mt-10) REVERT: B 219 LYS cc_start: 0.7500 (pttt) cc_final: 0.7038 (pttt) REVERT: B 262 GLN cc_start: 0.7598 (mt0) cc_final: 0.7207 (mt0) REVERT: B 263 TYR cc_start: 0.8212 (t80) cc_final: 0.7800 (t80) REVERT: B 305 LYS cc_start: 0.8508 (ptpp) cc_final: 0.7992 (ptpp) REVERT: C 38 MET cc_start: 0.7966 (mmt) cc_final: 0.7415 (mmt) REVERT: C 77 THR cc_start: 0.8912 (p) cc_final: 0.8690 (p) REVERT: C 85 PHE cc_start: 0.6792 (p90) cc_final: 0.6343 (p90) REVERT: C 114 MET cc_start: 0.7071 (mmm) cc_final: 0.6440 (mtm) REVERT: C 125 SER cc_start: 0.8556 (p) cc_final: 0.8209 (t) REVERT: C 149 ASP cc_start: 0.8574 (m-30) cc_final: 0.8320 (m-30) REVERT: C 199 LEU cc_start: 0.8681 (tp) cc_final: 0.8477 (tp) REVERT: C 247 THR cc_start: 0.8166 (p) cc_final: 0.7932 (p) REVERT: C 303 PHE cc_start: 0.7134 (m-80) cc_final: 0.6925 (m-80) REVERT: C 316 ASN cc_start: 0.7777 (t0) cc_final: 0.7547 (t0) REVERT: D 205 MET cc_start: 0.2019 (mtm) cc_final: 0.1671 (mtm) REVERT: E 142 ARG cc_start: 0.5110 (mtp85) cc_final: 0.4630 (mtp85) REVERT: F 135 GLU cc_start: 0.7810 (mp0) cc_final: 0.7411 (mp0) REVERT: F 150 GLN cc_start: 0.6567 (tt0) cc_final: 0.5827 (tt0) REVERT: F 151 ASN cc_start: 0.7826 (t0) cc_final: 0.7541 (p0) REVERT: F 152 TYR cc_start: 0.8437 (m-80) cc_final: 0.7503 (m-80) REVERT: F 166 VAL cc_start: 0.6555 (m) cc_final: 0.6271 (p) REVERT: F 318 GLN cc_start: 0.8151 (tt0) cc_final: 0.7910 (tt0) REVERT: F 337 ASN cc_start: 0.7096 (t0) cc_final: 0.6542 (t0) REVERT: F 345 LEU cc_start: 0.7238 (tt) cc_final: 0.6142 (pp) REVERT: F 487 ARG cc_start: 0.6315 (mtt-85) cc_final: 0.6090 (mtt180) REVERT: F 513 ASP cc_start: 0.7080 (m-30) cc_final: 0.6524 (t0) REVERT: F 515 ASP cc_start: 0.8078 (m-30) cc_final: 0.7873 (m-30) REVERT: F 548 ASP cc_start: 0.6343 (m-30) cc_final: 0.5513 (t0) REVERT: F 565 ILE cc_start: 0.3545 (mp) cc_final: 0.2817 (mp) outliers start: 2 outliers final: 2 residues processed: 452 average time/residue: 0.3216 time to fit residues: 215.4717 Evaluate side-chains 445 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 443 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 219 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 230 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 ASN ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.221206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.171557 restraints weight = 174471.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.182117 restraints weight = 88212.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.188687 restraints weight = 49728.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.192866 restraints weight = 30560.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.195318 restraints weight = 20091.734| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4497 r_free = 0.4497 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4497 r_free = 0.4497 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.4497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 18961 Z= 0.254 Angle : 0.648 8.258 25746 Z= 0.364 Chirality : 0.045 0.216 2697 Planarity : 0.005 0.078 3458 Dihedral : 5.248 32.932 2678 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.16 % Allowed : 1.83 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.17), residues: 2401 helix: 0.77 (0.32), residues: 255 sheet: -0.60 (0.15), residues: 1109 loop : -1.06 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 389 TYR 0.023 0.002 TYR B 90 PHE 0.027 0.002 PHE C 45 TRP 0.016 0.002 TRP F 516 HIS 0.009 0.002 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00496 (18960) covalent geometry : angle 0.64769 (25744) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.36829 ( 2) hydrogen bonds : bond 0.04472 ( 936) hydrogen bonds : angle 6.21605 ( 2628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8328 (tp) cc_final: 0.8044 (tp) REVERT: A 38 MET cc_start: 0.7985 (mmt) cc_final: 0.7494 (mmt) REVERT: A 90 TYR cc_start: 0.7526 (t80) cc_final: 0.6942 (t80) REVERT: A 98 TYR cc_start: 0.7872 (t80) cc_final: 0.7242 (t80) REVERT: A 115 LEU cc_start: 0.8441 (mm) cc_final: 0.8133 (mm) REVERT: A 129 PHE cc_start: 0.7073 (m-80) cc_final: 0.6538 (m-80) REVERT: A 156 GLN cc_start: 0.7819 (tt0) cc_final: 0.7596 (tt0) REVERT: A 160 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8704 (ttpp) REVERT: A 161 ASN cc_start: 0.8542 (t0) cc_final: 0.8099 (t0) REVERT: A 267 PHE cc_start: 0.8577 (p90) cc_final: 0.8263 (p90) REVERT: A 281 LYS cc_start: 0.8663 (mttp) cc_final: 0.8267 (mttp) REVERT: A 307 MET cc_start: 0.7765 (tpp) cc_final: 0.7424 (tpp) REVERT: A 310 TYR cc_start: 0.7855 (p90) cc_final: 0.7174 (p90) REVERT: B 4 TYR cc_start: 0.7583 (t80) cc_final: 0.6830 (t80) REVERT: B 6 LYS cc_start: 0.8184 (tttm) cc_final: 0.7965 (ttpp) REVERT: B 9 ASN cc_start: 0.6621 (t0) cc_final: 0.6402 (t0) REVERT: B 40 TYR cc_start: 0.7604 (p90) cc_final: 0.7289 (p90) REVERT: B 45 PHE cc_start: 0.7418 (p90) cc_final: 0.7197 (p90) REVERT: B 66 GLN cc_start: 0.6515 (mm110) cc_final: 0.6259 (mm110) REVERT: B 79 ASN cc_start: 0.7740 (m-40) cc_final: 0.7235 (m-40) REVERT: B 97 ASP cc_start: 0.8155 (p0) cc_final: 0.7934 (p0) REVERT: B 109 LEU cc_start: 0.8077 (mt) cc_final: 0.7770 (mt) REVERT: B 114 MET cc_start: 0.8134 (tpt) cc_final: 0.7870 (tpt) REVERT: B 164 ASP cc_start: 0.8382 (p0) cc_final: 0.7860 (p0) REVERT: B 183 GLU cc_start: 0.8135 (tt0) cc_final: 0.7092 (mt-10) REVERT: B 201 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8156 (mt-10) REVERT: B 219 LYS cc_start: 0.7637 (pttt) cc_final: 0.7172 (pttt) REVERT: B 262 GLN cc_start: 0.7735 (mt0) cc_final: 0.7506 (mt0) REVERT: B 263 TYR cc_start: 0.8343 (t80) cc_final: 0.8050 (t80) REVERT: B 270 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7568 (ttm110) REVERT: B 295 PHE cc_start: 0.7335 (m-10) cc_final: 0.7036 (m-10) REVERT: B 305 LYS cc_start: 0.8620 (ptpp) cc_final: 0.7986 (ptpp) REVERT: C 49 THR cc_start: 0.8051 (t) cc_final: 0.7701 (t) REVERT: C 85 PHE cc_start: 0.6948 (p90) cc_final: 0.6446 (p90) REVERT: C 114 MET cc_start: 0.7300 (mmm) cc_final: 0.6724 (mtm) REVERT: C 149 ASP cc_start: 0.8742 (m-30) cc_final: 0.8504 (m-30) REVERT: C 160 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8647 (ttmt) REVERT: C 207 ASN cc_start: 0.8047 (t0) cc_final: 0.7549 (p0) REVERT: C 303 PHE cc_start: 0.7103 (m-80) cc_final: 0.6896 (m-80) REVERT: C 316 ASN cc_start: 0.7768 (t0) cc_final: 0.7506 (t0) REVERT: C 319 ASP cc_start: 0.8002 (p0) cc_final: 0.7673 (p0) REVERT: C 321 ASP cc_start: 0.6592 (p0) cc_final: 0.6230 (p0) REVERT: D 205 MET cc_start: 0.2697 (mtm) cc_final: 0.2230 (mtm) REVERT: E 142 ARG cc_start: 0.5053 (mtp85) cc_final: 0.4605 (mtp85) REVERT: F 166 VAL cc_start: 0.6945 (m) cc_final: 0.6643 (p) REVERT: F 329 VAL cc_start: 0.3697 (t) cc_final: 0.3416 (t) REVERT: F 345 LEU cc_start: 0.7631 (tt) cc_final: 0.6492 (pp) REVERT: F 512 TYR cc_start: 0.5006 (m-10) cc_final: 0.4779 (m-10) REVERT: F 513 ASP cc_start: 0.7206 (m-30) cc_final: 0.6667 (t0) REVERT: F 548 ASP cc_start: 0.6407 (m-30) cc_final: 0.5594 (t0) REVERT: F 565 ILE cc_start: 0.3595 (mp) cc_final: 0.2828 (mp) outliers start: 1 outliers final: 0 residues processed: 458 average time/residue: 0.3318 time to fit residues: 223.5666 Evaluate side-chains 435 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 101 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 236 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.221125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.170329 restraints weight = 183899.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.181843 restraints weight = 93836.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.189313 restraints weight = 52294.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.193456 restraints weight = 31444.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.195921 restraints weight = 20709.573| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4521 r_free = 0.4521 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4521 r_free = 0.4521 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| r_final: 0.4521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 18961 Z= 0.243 Angle : 0.630 8.063 25746 Z= 0.355 Chirality : 0.045 0.200 2697 Planarity : 0.005 0.080 3458 Dihedral : 5.293 31.037 2678 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.16 % Allowed : 1.73 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.17), residues: 2401 helix: 0.82 (0.32), residues: 250 sheet: -0.59 (0.15), residues: 1084 loop : -1.14 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 487 TYR 0.052 0.002 TYR B 313 PHE 0.018 0.002 PHE C 23 TRP 0.031 0.002 TRP B 61 HIS 0.009 0.002 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00472 (18960) covalent geometry : angle 0.62987 (25744) SS BOND : bond 0.00027 ( 1) SS BOND : angle 1.97706 ( 2) hydrogen bonds : bond 0.04398 ( 936) hydrogen bonds : angle 6.25634 ( 2628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 463 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8374 (tp) cc_final: 0.8098 (tp) REVERT: A 38 MET cc_start: 0.7989 (mmt) cc_final: 0.7667 (mmt) REVERT: A 90 TYR cc_start: 0.7336 (t80) cc_final: 0.6920 (t80) REVERT: A 98 TYR cc_start: 0.8036 (t80) cc_final: 0.7333 (t80) REVERT: A 105 VAL cc_start: 0.8107 (t) cc_final: 0.7760 (t) REVERT: A 114 MET cc_start: 0.6975 (mtt) cc_final: 0.6687 (mtt) REVERT: A 117 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 160 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8698 (ttpp) REVERT: A 161 ASN cc_start: 0.8689 (t0) cc_final: 0.8333 (t0) REVERT: A 267 PHE cc_start: 0.8422 (p90) cc_final: 0.8121 (p90) REVERT: B 4 TYR cc_start: 0.7451 (t80) cc_final: 0.6750 (t80) REVERT: B 6 LYS cc_start: 0.8280 (tttm) cc_final: 0.8039 (ttpp) REVERT: B 9 ASN cc_start: 0.6896 (t0) cc_final: 0.6573 (t0) REVERT: B 40 TYR cc_start: 0.7687 (p90) cc_final: 0.7225 (p90) REVERT: B 66 GLN cc_start: 0.6801 (mm110) cc_final: 0.6420 (mm110) REVERT: B 79 ASN cc_start: 0.7666 (m-40) cc_final: 0.7147 (m-40) REVERT: B 80 LYS cc_start: 0.8995 (ptpp) cc_final: 0.8521 (ptpp) REVERT: B 97 ASP cc_start: 0.8116 (p0) cc_final: 0.7805 (p0) REVERT: B 109 LEU cc_start: 0.8208 (mt) cc_final: 0.7966 (mt) REVERT: B 114 MET cc_start: 0.8027 (tpt) cc_final: 0.7810 (tpt) REVERT: B 126 ASP cc_start: 0.7788 (m-30) cc_final: 0.7401 (m-30) REVERT: B 183 GLU cc_start: 0.8065 (tt0) cc_final: 0.6997 (mt-10) REVERT: B 201 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 219 LYS cc_start: 0.7549 (pttt) cc_final: 0.7044 (pttt) REVERT: B 262 GLN cc_start: 0.7694 (mt0) cc_final: 0.7257 (mt0) REVERT: B 263 TYR cc_start: 0.8249 (t80) cc_final: 0.7986 (t80) REVERT: B 305 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8089 (ptpp) REVERT: C 49 THR cc_start: 0.8040 (t) cc_final: 0.7803 (t) REVERT: C 85 PHE cc_start: 0.6764 (p90) cc_final: 0.6503 (p90) REVERT: C 89 LYS cc_start: 0.8172 (tttt) cc_final: 0.7869 (tttt) REVERT: C 114 MET cc_start: 0.7337 (mmm) cc_final: 0.6871 (mtm) REVERT: C 149 ASP cc_start: 0.8813 (m-30) cc_final: 0.8563 (m-30) REVERT: C 160 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8618 (ttmt) REVERT: C 207 ASN cc_start: 0.8175 (t0) cc_final: 0.7671 (p0) REVERT: C 303 PHE cc_start: 0.7310 (m-80) cc_final: 0.7007 (m-80) REVERT: C 316 ASN cc_start: 0.7842 (t0) cc_final: 0.7578 (t0) REVERT: C 319 ASP cc_start: 0.7626 (p0) cc_final: 0.7289 (p0) REVERT: C 321 ASP cc_start: 0.6197 (p0) cc_final: 0.5867 (p0) REVERT: D 205 MET cc_start: 0.2870 (mtm) cc_final: 0.2438 (mtm) REVERT: E 142 ARG cc_start: 0.5072 (mtp85) cc_final: 0.4660 (mtp85) REVERT: F 166 VAL cc_start: 0.7108 (m) cc_final: 0.6833 (p) REVERT: F 246 TYR cc_start: 0.7194 (t80) cc_final: 0.6959 (t80) REVERT: F 266 ILE cc_start: 0.7753 (mt) cc_final: 0.7407 (mt) REVERT: F 345 LEU cc_start: 0.7582 (tt) cc_final: 0.6650 (pp) REVERT: F 545 SER cc_start: 0.8276 (m) cc_final: 0.8014 (p) REVERT: F 548 ASP cc_start: 0.6259 (m-30) cc_final: 0.5565 (t0) REVERT: F 565 ILE cc_start: 0.3893 (mp) cc_final: 0.2772 (mp) REVERT: F 592 TYR cc_start: 0.6841 (t80) cc_final: 0.6396 (t80) outliers start: 1 outliers final: 0 residues processed: 463 average time/residue: 0.3302 time to fit residues: 225.2971 Evaluate side-chains 441 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 225 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 234 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN E 290 ASN E 334 ASN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.224443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.166467 restraints weight = 201002.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.180116 restraints weight = 101692.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.187199 restraints weight = 58319.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.193135 restraints weight = 34298.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.194772 restraints weight = 20287.977| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4523 r_free = 0.4523 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4523 r_free = 0.4523 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| r_final: 0.4523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18961 Z= 0.177 Angle : 0.577 7.056 25746 Z= 0.323 Chirality : 0.045 0.199 2697 Planarity : 0.005 0.136 3458 Dihedral : 5.130 29.832 2678 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.10 % Allowed : 0.99 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.17), residues: 2401 helix: 1.10 (0.32), residues: 250 sheet: -0.55 (0.15), residues: 1096 loop : -1.08 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 140 TYR 0.025 0.002 TYR B 313 PHE 0.016 0.001 PHE F 514 TRP 0.020 0.002 TRP B 61 HIS 0.010 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00348 (18960) covalent geometry : angle 0.57655 (25744) SS BOND : bond 0.00001 ( 1) SS BOND : angle 2.14272 ( 2) hydrogen bonds : bond 0.03893 ( 936) hydrogen bonds : angle 6.06675 ( 2628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8324 (tp) cc_final: 0.8068 (tp) REVERT: A 16 LYS cc_start: 0.8234 (ptpt) cc_final: 0.7972 (ptpt) REVERT: A 38 MET cc_start: 0.7981 (mmt) cc_final: 0.7720 (mmt) REVERT: A 65 PHE cc_start: 0.7380 (m-10) cc_final: 0.7160 (m-10) REVERT: A 85 PHE cc_start: 0.7024 (p90) cc_final: 0.5992 (p90) REVERT: A 98 TYR cc_start: 0.8000 (t80) cc_final: 0.7507 (t80) REVERT: A 101 ASN cc_start: 0.7412 (t0) cc_final: 0.7031 (t0) REVERT: A 105 VAL cc_start: 0.7912 (t) cc_final: 0.7441 (t) REVERT: A 109 LEU cc_start: 0.8545 (mt) cc_final: 0.8344 (mt) REVERT: A 114 MET cc_start: 0.6795 (mtt) cc_final: 0.6526 (mtt) REVERT: A 160 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8584 (ttpp) REVERT: A 161 ASN cc_start: 0.8744 (t0) cc_final: 0.8386 (t0) REVERT: A 201 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7574 (mt-10) REVERT: A 267 PHE cc_start: 0.8325 (p90) cc_final: 0.8072 (p90) REVERT: A 292 VAL cc_start: 0.8562 (m) cc_final: 0.8178 (m) REVERT: A 307 MET cc_start: 0.7502 (tpp) cc_final: 0.7252 (tpp) REVERT: B 4 TYR cc_start: 0.7375 (t80) cc_final: 0.6671 (t80) REVERT: B 6 LYS cc_start: 0.8274 (tttm) cc_final: 0.7939 (ttpp) REVERT: B 9 ASN cc_start: 0.6932 (t0) cc_final: 0.6533 (t0) REVERT: B 40 TYR cc_start: 0.7695 (p90) cc_final: 0.7364 (p90) REVERT: B 79 ASN cc_start: 0.7786 (m-40) cc_final: 0.7248 (m-40) REVERT: B 80 LYS cc_start: 0.8955 (ptpp) cc_final: 0.8458 (ptpp) REVERT: B 97 ASP cc_start: 0.8012 (p0) cc_final: 0.7726 (p0) REVERT: B 109 LEU cc_start: 0.8186 (mt) cc_final: 0.7935 (mt) REVERT: B 114 MET cc_start: 0.7981 (tpt) cc_final: 0.7736 (tpt) REVERT: B 183 GLU cc_start: 0.8008 (tt0) cc_final: 0.6977 (mt-10) REVERT: B 196 ARG cc_start: 0.7468 (mtp-110) cc_final: 0.7249 (mtp-110) REVERT: B 201 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 207 ASN cc_start: 0.7164 (m-40) cc_final: 0.6915 (m-40) REVERT: B 219 LYS cc_start: 0.7499 (pttt) cc_final: 0.6975 (pttt) REVERT: B 224 ASN cc_start: 0.8492 (m-40) cc_final: 0.7948 (m110) REVERT: B 262 GLN cc_start: 0.7646 (mt0) cc_final: 0.7254 (mt0) REVERT: B 263 TYR cc_start: 0.8199 (t80) cc_final: 0.7916 (t80) REVERT: B 295 PHE cc_start: 0.6999 (m-10) cc_final: 0.6701 (m-10) REVERT: B 305 LYS cc_start: 0.8580 (ptpp) cc_final: 0.8377 (ptpp) REVERT: C 85 PHE cc_start: 0.6712 (p90) cc_final: 0.6475 (p90) REVERT: C 89 LYS cc_start: 0.8096 (tttt) cc_final: 0.7747 (tttt) REVERT: C 114 MET cc_start: 0.7263 (mmm) cc_final: 0.6915 (mtm) REVERT: C 149 ASP cc_start: 0.8766 (m-30) cc_final: 0.8459 (m-30) REVERT: C 160 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8672 (ttmt) REVERT: C 207 ASN cc_start: 0.8175 (t0) cc_final: 0.7700 (p0) REVERT: C 247 THR cc_start: 0.7715 (p) cc_final: 0.7452 (p) REVERT: C 281 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7364 (mtmm) REVERT: C 282 ASP cc_start: 0.7130 (m-30) cc_final: 0.6850 (m-30) REVERT: C 303 PHE cc_start: 0.7308 (m-80) cc_final: 0.6994 (m-80) REVERT: C 316 ASN cc_start: 0.7810 (t0) cc_final: 0.7531 (t0) REVERT: C 319 ASP cc_start: 0.7575 (p0) cc_final: 0.7232 (p0) REVERT: C 321 ASP cc_start: 0.6005 (p0) cc_final: 0.5663 (p0) REVERT: D 205 MET cc_start: 0.2329 (mtm) cc_final: 0.2056 (mtm) REVERT: E 142 ARG cc_start: 0.5026 (mtp85) cc_final: 0.4594 (mtp85) REVERT: F 166 VAL cc_start: 0.7135 (m) cc_final: 0.6861 (p) REVERT: F 266 ILE cc_start: 0.7721 (mt) cc_final: 0.7503 (mt) REVERT: F 333 TYR cc_start: 0.6430 (m-80) cc_final: 0.5802 (m-80) REVERT: F 548 ASP cc_start: 0.6164 (m-30) cc_final: 0.5496 (t0) REVERT: F 565 ILE cc_start: 0.3802 (mp) cc_final: 0.3208 (mp) REVERT: F 592 TYR cc_start: 0.6765 (t80) cc_final: 0.6363 (t80) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.3301 time to fit residues: 214.3637 Evaluate side-chains 430 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 106 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 151 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.217026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.168281 restraints weight = 187836.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.179404 restraints weight = 95501.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.186525 restraints weight = 53555.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.190829 restraints weight = 32348.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.193386 restraints weight = 21102.291| |-----------------------------------------------------------------------------| r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4491 r_free = 0.4491 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4491 r_free = 0.4491 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| r_final: 0.4491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 18961 Z= 0.264 Angle : 0.676 11.365 25746 Z= 0.380 Chirality : 0.046 0.186 2697 Planarity : 0.005 0.085 3458 Dihedral : 5.486 37.191 2678 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.10 % Allowed : 0.89 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.17), residues: 2401 helix: 0.62 (0.31), residues: 259 sheet: -0.73 (0.15), residues: 1091 loop : -1.25 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 526 TYR 0.024 0.002 TYR B 313 PHE 0.035 0.002 PHE E 219 TRP 0.032 0.002 TRP B 61 HIS 0.010 0.002 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00525 (18960) covalent geometry : angle 0.67564 (25744) SS BOND : bond 0.01607 ( 1) SS BOND : angle 2.40925 ( 2) hydrogen bonds : bond 0.04624 ( 936) hydrogen bonds : angle 6.37670 ( 2628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8268 (tp) cc_final: 0.8000 (tp) REVERT: A 16 LYS cc_start: 0.8303 (ptpt) cc_final: 0.8061 (ptpt) REVERT: A 65 PHE cc_start: 0.7533 (m-10) cc_final: 0.7301 (m-10) REVERT: A 105 VAL cc_start: 0.7932 (t) cc_final: 0.7513 (t) REVERT: A 117 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 160 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8738 (ttpp) REVERT: A 161 ASN cc_start: 0.8817 (t0) cc_final: 0.8448 (t0) REVERT: A 201 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7774 (mt-10) REVERT: A 203 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8401 (tp-100) REVERT: A 267 PHE cc_start: 0.8508 (p90) cc_final: 0.8264 (p90) REVERT: A 293 ASN cc_start: 0.7572 (m110) cc_final: 0.7201 (p0) REVERT: A 318 ILE cc_start: 0.8963 (mm) cc_final: 0.8562 (mm) REVERT: A 337 VAL cc_start: 0.6559 (t) cc_final: 0.6320 (t) REVERT: B 4 TYR cc_start: 0.7404 (t80) cc_final: 0.6623 (t80) REVERT: B 9 ASN cc_start: 0.6884 (t0) cc_final: 0.6306 (t0) REVERT: B 16 LYS cc_start: 0.7959 (pttt) cc_final: 0.7670 (pttt) REVERT: B 40 TYR cc_start: 0.7801 (p90) cc_final: 0.7248 (p90) REVERT: B 64 ASN cc_start: 0.8029 (t0) cc_final: 0.7811 (m-40) REVERT: B 66 GLN cc_start: 0.6906 (mm110) cc_final: 0.6493 (mm110) REVERT: B 79 ASN cc_start: 0.7643 (m-40) cc_final: 0.7039 (m-40) REVERT: B 80 LYS cc_start: 0.9017 (ptpp) cc_final: 0.8537 (ptpp) REVERT: B 109 LEU cc_start: 0.8278 (mt) cc_final: 0.8045 (mt) REVERT: B 126 ASP cc_start: 0.7816 (m-30) cc_final: 0.7411 (m-30) REVERT: B 183 GLU cc_start: 0.8049 (tt0) cc_final: 0.7105 (mt-10) REVERT: B 201 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 207 ASN cc_start: 0.7429 (m-40) cc_final: 0.7196 (m-40) REVERT: B 219 LYS cc_start: 0.7622 (pttt) cc_final: 0.7106 (pttt) REVERT: B 262 GLN cc_start: 0.7741 (mt0) cc_final: 0.7351 (mt0) REVERT: B 295 PHE cc_start: 0.7082 (m-10) cc_final: 0.6866 (m-10) REVERT: B 306 ASN cc_start: 0.8418 (m-40) cc_final: 0.8126 (m110) REVERT: C 38 MET cc_start: 0.8075 (mmt) cc_final: 0.7620 (mmt) REVERT: C 85 PHE cc_start: 0.6825 (p90) cc_final: 0.6593 (p90) REVERT: C 89 LYS cc_start: 0.8270 (tttt) cc_final: 0.7922 (tttt) REVERT: C 109 LEU cc_start: 0.9073 (mt) cc_final: 0.8851 (mt) REVERT: C 114 MET cc_start: 0.7451 (mmm) cc_final: 0.7075 (mtm) REVERT: C 121 ASP cc_start: 0.8459 (p0) cc_final: 0.8215 (p0) REVERT: C 149 ASP cc_start: 0.8913 (m-30) cc_final: 0.8679 (m-30) REVERT: C 160 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8713 (ttmt) REVERT: C 207 ASN cc_start: 0.8257 (t0) cc_final: 0.7808 (p0) REVERT: C 281 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7568 (mtmm) REVERT: C 282 ASP cc_start: 0.7089 (m-30) cc_final: 0.6797 (m-30) REVERT: C 303 PHE cc_start: 0.7369 (m-80) cc_final: 0.7043 (m-80) REVERT: C 316 ASN cc_start: 0.7827 (t0) cc_final: 0.7571 (t0) REVERT: C 319 ASP cc_start: 0.7873 (p0) cc_final: 0.7590 (p0) REVERT: C 321 ASP cc_start: 0.6069 (p0) cc_final: 0.5689 (p0) REVERT: D 205 MET cc_start: 0.4217 (mtm) cc_final: 0.3455 (mtm) REVERT: E 142 ARG cc_start: 0.5031 (mtp85) cc_final: 0.4525 (mtp85) REVERT: F 166 VAL cc_start: 0.7325 (m) cc_final: 0.7084 (p) REVERT: F 305 ILE cc_start: 0.7338 (mt) cc_final: 0.7128 (mt) REVERT: F 397 ASN cc_start: 0.4325 (p0) cc_final: 0.3944 (p0) REVERT: F 548 ASP cc_start: 0.6166 (m-30) cc_final: 0.5534 (t0) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.3287 time to fit residues: 217.0600 Evaluate side-chains 441 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 172 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.220833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.169576 restraints weight = 176506.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.181257 restraints weight = 90920.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.188690 restraints weight = 50853.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.192822 restraints weight = 30627.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.195182 restraints weight = 20313.646| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4515 r_free = 0.4515 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4515 r_free = 0.4515 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| r_final: 0.4515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18961 Z= 0.176 Angle : 0.589 7.051 25746 Z= 0.329 Chirality : 0.045 0.201 2697 Planarity : 0.005 0.067 3458 Dihedral : 5.256 35.513 2678 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.16 % Allowed : 0.52 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2401 helix: 0.93 (0.32), residues: 259 sheet: -0.68 (0.15), residues: 1090 loop : -1.16 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 526 TYR 0.021 0.002 TYR B 63 PHE 0.027 0.002 PHE B 65 TRP 0.016 0.001 TRP B 61 HIS 0.008 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00349 (18960) covalent geometry : angle 0.58850 (25744) SS BOND : bond 0.00286 ( 1) SS BOND : angle 2.12901 ( 2) hydrogen bonds : bond 0.03912 ( 936) hydrogen bonds : angle 6.16514 ( 2628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8246 (tp) cc_final: 0.8002 (tp) REVERT: A 16 LYS cc_start: 0.8230 (ptpt) cc_final: 0.7999 (ptpt) REVERT: A 65 PHE cc_start: 0.7468 (m-10) cc_final: 0.7049 (m-10) REVERT: A 85 PHE cc_start: 0.7161 (p90) cc_final: 0.6109 (p90) REVERT: A 98 TYR cc_start: 0.7789 (t80) cc_final: 0.7124 (t80) REVERT: A 101 ASN cc_start: 0.7568 (t0) cc_final: 0.7305 (t0) REVERT: A 105 VAL cc_start: 0.7863 (t) cc_final: 0.7417 (t) REVERT: A 109 LEU cc_start: 0.8538 (mt) cc_final: 0.8303 (mt) REVERT: A 160 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8624 (ttpp) REVERT: A 161 ASN cc_start: 0.8758 (t0) cc_final: 0.8309 (t0) REVERT: A 201 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 267 PHE cc_start: 0.8497 (p90) cc_final: 0.8262 (p90) REVERT: A 337 VAL cc_start: 0.6526 (t) cc_final: 0.6254 (t) REVERT: B 4 TYR cc_start: 0.7362 (t80) cc_final: 0.6633 (t80) REVERT: B 6 LYS cc_start: 0.8165 (tttm) cc_final: 0.7850 (tttp) REVERT: B 9 ASN cc_start: 0.6791 (t0) cc_final: 0.6189 (t0) REVERT: B 16 LYS cc_start: 0.7958 (pttt) cc_final: 0.7664 (pttt) REVERT: B 40 TYR cc_start: 0.7925 (p90) cc_final: 0.7414 (p90) REVERT: B 66 GLN cc_start: 0.7063 (mm110) cc_final: 0.6356 (mm110) REVERT: B 76 GLN cc_start: 0.8361 (mp10) cc_final: 0.8133 (mp10) REVERT: B 79 ASN cc_start: 0.7740 (m-40) cc_final: 0.7157 (m-40) REVERT: B 80 LYS cc_start: 0.9001 (ptpp) cc_final: 0.8504 (ptpp) REVERT: B 109 LEU cc_start: 0.8285 (mt) cc_final: 0.8023 (mt) REVERT: B 126 ASP cc_start: 0.7810 (m-30) cc_final: 0.7345 (m-30) REVERT: B 183 GLU cc_start: 0.7937 (tt0) cc_final: 0.7003 (mt-10) REVERT: B 196 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.7240 (mtp-110) REVERT: B 201 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8249 (mt-10) REVERT: B 219 LYS cc_start: 0.7605 (pttt) cc_final: 0.7092 (pttt) REVERT: B 225 ILE cc_start: 0.7527 (mt) cc_final: 0.7167 (tp) REVERT: B 233 GLU cc_start: 0.5124 (tt0) cc_final: 0.4919 (tt0) REVERT: B 262 GLN cc_start: 0.7753 (mt0) cc_final: 0.7543 (mt0) REVERT: B 295 PHE cc_start: 0.7168 (m-10) cc_final: 0.6930 (m-10) REVERT: B 306 ASN cc_start: 0.8412 (m-40) cc_final: 0.8160 (m110) REVERT: C 38 MET cc_start: 0.8039 (mmt) cc_final: 0.7429 (mmt) REVERT: C 46 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7148 (mtmt) REVERT: C 49 THR cc_start: 0.7908 (t) cc_final: 0.7693 (t) REVERT: C 58 TYR cc_start: 0.7862 (p90) cc_final: 0.7384 (p90) REVERT: C 85 PHE cc_start: 0.6860 (p90) cc_final: 0.6556 (p90) REVERT: C 89 LYS cc_start: 0.8226 (tttt) cc_final: 0.7808 (tttt) REVERT: C 104 VAL cc_start: 0.8912 (m) cc_final: 0.8704 (m) REVERT: C 109 LEU cc_start: 0.8967 (mt) cc_final: 0.8706 (mt) REVERT: C 114 MET cc_start: 0.7408 (mmm) cc_final: 0.7108 (mtm) REVERT: C 149 ASP cc_start: 0.8811 (m-30) cc_final: 0.8543 (m-30) REVERT: C 160 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8541 (ttmt) REVERT: C 207 ASN cc_start: 0.8282 (t0) cc_final: 0.7872 (p0) REVERT: C 247 THR cc_start: 0.7902 (p) cc_final: 0.7621 (p) REVERT: C 281 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7570 (mtmm) REVERT: C 282 ASP cc_start: 0.7091 (m-30) cc_final: 0.6799 (m-30) REVERT: C 294 TYR cc_start: 0.7807 (p90) cc_final: 0.6850 (p90) REVERT: C 303 PHE cc_start: 0.7455 (m-80) cc_final: 0.6959 (m-80) REVERT: C 306 ASN cc_start: 0.8635 (m110) cc_final: 0.8025 (m-40) REVERT: C 319 ASP cc_start: 0.7844 (p0) cc_final: 0.7581 (p0) REVERT: C 321 ASP cc_start: 0.6225 (p0) cc_final: 0.5860 (p0) REVERT: D 205 MET cc_start: 0.3694 (mtm) cc_final: 0.3167 (mtm) REVERT: E 142 ARG cc_start: 0.5106 (mtp85) cc_final: 0.4709 (mtp85) REVERT: F 166 VAL cc_start: 0.7305 (m) cc_final: 0.7025 (p) REVERT: F 336 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7933 (mtt-85) REVERT: F 397 ASN cc_start: 0.4104 (p0) cc_final: 0.3738 (p0) REVERT: F 548 ASP cc_start: 0.6320 (m-30) cc_final: 0.5614 (t0) REVERT: F 565 ILE cc_start: 0.3762 (mp) cc_final: 0.2864 (mp) REVERT: F 592 TYR cc_start: 0.6815 (t80) cc_final: 0.6398 (t80) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.3320 time to fit residues: 223.7634 Evaluate side-chains 441 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 144 optimal weight: 50.0000 chunk 157 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 HIS B 52 ASN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.207595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.155552 restraints weight = 209822.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.167538 restraints weight = 101849.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.175533 restraints weight = 56547.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.180410 restraints weight = 33906.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.183510 restraints weight = 21969.538| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4418 r_free = 0.4418 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4418 r_free = 0.4418 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.4418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.132 18961 Z= 0.413 Angle : 0.842 9.968 25746 Z= 0.480 Chirality : 0.050 0.182 2697 Planarity : 0.007 0.138 3458 Dihedral : 6.226 45.985 2678 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.67 % Favored : 90.25 % Rotamer: Outliers : 0.16 % Allowed : 0.73 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2401 helix: -0.22 (0.30), residues: 259 sheet: -0.98 (0.15), residues: 1052 loop : -1.77 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 328 TYR 0.047 0.003 TYR C 63 PHE 0.039 0.003 PHE E 68 TRP 0.029 0.003 TRP B 61 HIS 0.020 0.003 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00814 (18960) covalent geometry : angle 0.84193 (25744) SS BOND : bond 0.00250 ( 1) SS BOND : angle 2.34028 ( 2) hydrogen bonds : bond 0.05863 ( 936) hydrogen bonds : angle 7.11696 ( 2628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 90 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 454 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8302 (tp) cc_final: 0.8047 (tp) REVERT: A 16 LYS cc_start: 0.8390 (ptpt) cc_final: 0.8147 (ptpt) REVERT: A 65 PHE cc_start: 0.7699 (m-10) cc_final: 0.7485 (m-10) REVERT: A 117 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 122 THR cc_start: 0.8861 (t) cc_final: 0.8310 (t) REVERT: A 160 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8723 (ttpp) REVERT: A 161 ASN cc_start: 0.8804 (t0) cc_final: 0.8364 (t0) REVERT: A 258 LEU cc_start: 0.7404 (mm) cc_final: 0.7187 (mm) REVERT: A 267 PHE cc_start: 0.8520 (p90) cc_final: 0.8198 (p90) REVERT: A 301 TYR cc_start: 0.8570 (t80) cc_final: 0.8219 (t80) REVERT: A 337 VAL cc_start: 0.6588 (t) cc_final: 0.6327 (t) REVERT: B 4 TYR cc_start: 0.7525 (t80) cc_final: 0.5295 (t80) REVERT: B 6 LYS cc_start: 0.8341 (tttm) cc_final: 0.7407 (ttpp) REVERT: B 9 ASN cc_start: 0.7033 (t0) cc_final: 0.6031 (t0) REVERT: B 76 GLN cc_start: 0.8406 (mp10) cc_final: 0.8187 (mp10) REVERT: B 80 LYS cc_start: 0.9047 (ptpp) cc_final: 0.8578 (ptpp) REVERT: B 100 ARG cc_start: 0.7947 (tpt-90) cc_final: 0.7521 (tpp80) REVERT: B 109 LEU cc_start: 0.8479 (mt) cc_final: 0.8192 (mt) REVERT: B 124 TYR cc_start: 0.7849 (m-80) cc_final: 0.7306 (m-80) REVERT: B 164 ASP cc_start: 0.8261 (p0) cc_final: 0.7752 (p0) REVERT: B 183 GLU cc_start: 0.8079 (tt0) cc_final: 0.7138 (mt-10) REVERT: B 201 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8373 (mt-10) REVERT: B 219 LYS cc_start: 0.7758 (pttt) cc_final: 0.7236 (pttt) REVERT: B 262 GLN cc_start: 0.7742 (mt0) cc_final: 0.7378 (mt0) REVERT: B 295 PHE cc_start: 0.6999 (m-10) cc_final: 0.6794 (m-10) REVERT: B 339 GLN cc_start: 0.8334 (pm20) cc_final: 0.8102 (pm20) REVERT: C 32 TYR cc_start: 0.7586 (t80) cc_final: 0.7163 (t80) REVERT: C 46 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7455 (mtmt) REVERT: C 49 THR cc_start: 0.7996 (t) cc_final: 0.7766 (t) REVERT: C 85 PHE cc_start: 0.6767 (p90) cc_final: 0.6521 (p90) REVERT: C 89 LYS cc_start: 0.8454 (tttt) cc_final: 0.8079 (tttt) REVERT: C 109 LEU cc_start: 0.9117 (mt) cc_final: 0.8889 (mt) REVERT: C 114 MET cc_start: 0.7621 (mmm) cc_final: 0.7344 (mtm) REVERT: C 149 ASP cc_start: 0.9024 (m-30) cc_final: 0.8765 (m-30) REVERT: C 207 ASN cc_start: 0.8377 (t0) cc_final: 0.7956 (p0) REVERT: C 221 ASP cc_start: 0.7345 (t0) cc_final: 0.6975 (t0) REVERT: C 224 ASN cc_start: 0.7236 (m-40) cc_final: 0.6964 (m-40) REVERT: C 282 ASP cc_start: 0.6952 (m-30) cc_final: 0.6708 (m-30) REVERT: C 316 ASN cc_start: 0.7800 (t0) cc_final: 0.7521 (t0) REVERT: C 319 ASP cc_start: 0.7914 (p0) cc_final: 0.7600 (p0) REVERT: C 321 ASP cc_start: 0.6026 (p0) cc_final: 0.5603 (p0) REVERT: D 205 MET cc_start: 0.4372 (mtm) cc_final: 0.3809 (mtm) REVERT: E 142 ARG cc_start: 0.5180 (mtp85) cc_final: 0.4578 (mtp85) REVERT: F 165 ARG cc_start: 0.7888 (ttp-110) cc_final: 0.7158 (ttp-170) REVERT: F 166 VAL cc_start: 0.7733 (m) cc_final: 0.7458 (p) REVERT: F 336 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7924 (mtt-85) REVERT: F 397 ASN cc_start: 0.4533 (p0) cc_final: 0.4181 (p0) REVERT: F 548 ASP cc_start: 0.6411 (m-30) cc_final: 0.5867 (t0) REVERT: F 565 ILE cc_start: 0.4236 (mp) cc_final: 0.2759 (mt) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.3241 time to fit residues: 218.8925 Evaluate side-chains 432 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.220407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.169546 restraints weight = 186992.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.181426 restraints weight = 95116.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.188975 restraints weight = 53082.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.193477 restraints weight = 31910.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.196270 restraints weight = 20943.200| |-----------------------------------------------------------------------------| r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.4502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18961 Z= 0.144 Angle : 0.600 6.797 25746 Z= 0.334 Chirality : 0.046 0.195 2697 Planarity : 0.005 0.059 3458 Dihedral : 5.516 34.022 2678 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.17), residues: 2401 helix: 0.76 (0.32), residues: 259 sheet: -0.76 (0.15), residues: 1087 loop : -1.44 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 526 TYR 0.020 0.002 TYR B 63 PHE 0.046 0.002 PHE B 65 TRP 0.020 0.001 TRP C 61 HIS 0.009 0.002 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00302 (18960) covalent geometry : angle 0.59909 (25744) SS BOND : bond 0.00257 ( 1) SS BOND : angle 2.80450 ( 2) hydrogen bonds : bond 0.03805 ( 936) hydrogen bonds : angle 6.33410 ( 2628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7230.53 seconds wall clock time: 123 minutes 42.46 seconds (7422.46 seconds total)