Starting phenix.real_space_refine on Sat Mar 23 06:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/03_2024/7nsu_12577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/03_2024/7nsu_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/03_2024/7nsu_12577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/03_2024/7nsu_12577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/03_2024/7nsu_12577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/03_2024/7nsu_12577.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 17.82, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.93 Conformation dependent library (CDL) restraints added in 4.3 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: 3.19 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: 15.47 Time building geometry restraints manager: 31.87 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: 98.30 - 105.45: 289 105.45 - 112.61: 39866 112.61 - 119.76: 10082 119.76 - 126.91: 14916 126.91 - 134.07: 192 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 1.850 nonbonded pdb=" OD2 ASP F 528 " pdb=" H TYR F 577 " model vdw 1.483 1.850 nonbonded pdb="HE22 GLN F 364 " pdb=" O PRO F 408 " model vdw 1.485 1.850 nonbonded pdb=" O VAL D 29 " pdb="HE22 GLN E 172 " model vdw 1.489 1.850 nonbonded pdb=" OE1 GLU D 167 " pdb=" H GLU D 167 " model vdw 1.523 1.850 ... (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 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: 1.110 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: 0.550 Extract box with map and model: 6.540 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 116.620 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.020 ------------------------------------------------------------------------------- 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 18960 Z= 0.218 Angle : 0.698 9.478 25744 Z= 0.401 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (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 TRP 0.023 0.002 TRP E 207 HIS 0.005 0.001 HIS D 388 PHE 0.017 0.002 PHE E 219 TYR 0.025 0.002 TYR D 324 ARG 0.007 0.001 ARG E 237 *********************** 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 fitting. rotamer outliers: 68 poor density : 492 time to evaluate : 2.806 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: A 16 LYS cc_start: 0.8140 (pttt) cc_final: 0.7883 (pttt) REVERT: A 38 MET cc_start: 0.8041 (mmt) cc_final: 0.7531 (mmt) REVERT: A 65 PHE cc_start: 0.7071 (m-80) cc_final: 0.6359 (m-80) REVERT: A 90 TYR cc_start: 0.7624 (t80) cc_final: 0.6824 (t80) REVERT: A 92 ASP cc_start: 0.8514 (p0) cc_final: 0.8067 (p0) REVERT: A 160 LYS cc_start: 0.8270 (ttmt) cc_final: 0.8036 (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: 0.6738 (mm) REVERT: A 267 PHE cc_start: 0.7909 (p90) cc_final: 0.7582 (p90) REVERT: A 310 TYR cc_start: 0.7545 (p90) cc_final: 0.7342 (p90) REVERT: A 330 ASP cc_start: 0.5006 (m-30) cc_final: 0.4727 (m-30) 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: 0.6384 (mm110) REVERT: B 100 ARG cc_start: 0.7438 (ttt90) cc_final: 0.7023 (tpt-90) REVERT: B 139 TYR cc_start: 0.7002 (t80) cc_final: 0.6705 (t80) REVERT: B 177 SER cc_start: 0.7123 (t) cc_final: 0.6836 (p) REVERT: B 201 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8251 (mt-10) REVERT: B 219 LYS cc_start: 0.7352 (pttt) cc_final: 0.7083 (pttt) REVERT: B 233 GLU cc_start: 0.5234 (tt0) cc_final: 0.4579 (tp30) REVERT: B 241 THR cc_start: 0.6694 (p) cc_final: 0.6457 (p) REVERT: B 262 GLN cc_start: 0.7256 (mt0) cc_final: 0.6896 (mt0) REVERT: B 263 TYR cc_start: 0.8074 (t80) cc_final: 0.7414 (t80) REVERT: B 289 VAL cc_start: 0.4976 (p) cc_final: 0.3970 (m) REVERT: B 295 PHE cc_start: 0.6886 (m-10) cc_final: 0.6662 (m-10) REVERT: B 311 VAL cc_start: 0.6522 (t) cc_final: 0.6321 (p) REVERT: C 38 MET cc_start: 0.7816 (mmt) cc_final: 0.7237 (mmt) REVERT: C 55 LEU cc_start: 0.8467 (tp) cc_final: 0.8001 (tp) REVERT: C 85 PHE cc_start: 0.6967 (p90) cc_final: 0.6470 (p90) REVERT: C 207 ASN cc_start: 0.7534 (t0) cc_final: 0.7310 (m110) REVERT: C 316 ASN cc_start: 0.7519 (t0) cc_final: 0.7247 (t0) REVERT: D 284 VAL cc_start: -0.0338 (OUTLIER) cc_final: -0.0574 (t) REVERT: E 142 ARG cc_start: 0.4112 (mtp85) cc_final: 0.3864 (mtp85) REVERT: F 150 GLN cc_start: 0.5491 (pt0) cc_final: 0.4825 (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: 0.6587 (t0) REVERT: F 157 GLN cc_start: 0.5351 (OUTLIER) cc_final: 0.4805 (pt0) REVERT: F 176 HIS cc_start: 0.5126 (m90) cc_final: 0.4784 (m90) REVERT: F 261 ILE cc_start: 0.4603 (pt) cc_final: 0.4143 (tp) REVERT: F 262 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6816 (mmtm) REVERT: F 266 ILE cc_start: 0.7929 (mt) cc_final: 0.6913 (mt) REVERT: F 293 MET cc_start: 0.5196 (tmm) cc_final: 0.4964 (mmm) REVERT: F 305 ILE cc_start: 0.7062 (mm) cc_final: 0.6840 (mt) REVERT: F 487 ARG cc_start: 0.6005 (mtt-85) cc_final: 0.5720 (mtm110) REVERT: F 513 ASP cc_start: 0.6283 (m-30) cc_final: 0.6042 (t0) REVERT: F 548 ASP cc_start: 0.6479 (m-30) cc_final: 0.5786 (t0) REVERT: F 565 ILE cc_start: 0.3653 (mp) cc_final: 0.3286 (mp) outliers start: 68 outliers final: 35 residues processed: 547 average time/residue: 0.7410 time to fit residues: 586.9867 Evaluate side-chains 484 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 446 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 50.0000 chunk 140 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 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** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 18960 Z= 0.440 Angle : 0.803 10.157 25744 Z= 0.453 Chirality : 0.048 0.203 2697 Planarity : 0.007 0.122 3458 Dihedral : 5.657 27.501 2678 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 0.31 % Allowed : 3.35 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2401 helix: -0.56 (0.29), residues: 262 sheet: -0.40 (0.15), residues: 1098 loop : -1.21 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 426 HIS 0.018 0.003 HIS D 315 PHE 0.025 0.003 PHE C 23 TYR 0.031 0.003 TYR B 63 ARG 0.014 0.001 ARG D 274 *********************** 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 470 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 465 time to evaluate : 2.736 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: A 38 MET cc_start: 0.8524 (mmt) cc_final: 0.7784 (mmm) REVERT: A 65 PHE cc_start: 0.6804 (m-80) cc_final: 0.6538 (m-80) REVERT: A 90 TYR cc_start: 0.7629 (t80) cc_final: 0.7025 (t80) REVERT: A 92 ASP cc_start: 0.8598 (p0) cc_final: 0.8063 (p0) REVERT: A 129 PHE cc_start: 0.6845 (m-80) cc_final: 0.6407 (m-80) REVERT: A 181 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6977 (tp30) REVERT: A 258 LEU cc_start: 0.7128 (mm) cc_final: 0.6907 (mm) REVERT: A 267 PHE cc_start: 0.8318 (p90) cc_final: 0.8079 (p90) REVERT: A 281 LYS cc_start: 0.8813 (mttp) cc_final: 0.8313 (mttp) REVERT: A 303 PHE cc_start: 0.8424 (m-80) cc_final: 0.7568 (m-80) REVERT: A 307 MET cc_start: 0.7768 (tpp) cc_final: 0.7269 (tpp) REVERT: A 310 TYR cc_start: 0.7632 (p90) cc_final: 0.7174 (p90) REVERT: A 318 ILE cc_start: 0.8619 (mm) cc_final: 0.8353 (mm) REVERT: A 321 ASP cc_start: 0.7180 (m-30) cc_final: 0.6977 (m-30) REVERT: B 46 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7243 (mtpt) REVERT: B 124 TYR cc_start: 0.7547 (m-80) cc_final: 0.7155 (m-80) REVERT: B 138 THR cc_start: 0.7585 (m) cc_final: 0.7222 (m) REVERT: B 164 ASP cc_start: 0.7935 (p0) cc_final: 0.7644 (p0) REVERT: B 177 SER cc_start: 0.7276 (t) cc_final: 0.7022 (p) REVERT: B 183 GLU cc_start: 0.8315 (tt0) cc_final: 0.7292 (mt-10) REVERT: B 191 TYR cc_start: 0.7495 (t80) cc_final: 0.6778 (t80) REVERT: B 201 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 224 ASN cc_start: 0.9038 (m-40) cc_final: 0.8652 (m-40) REVERT: B 233 GLU cc_start: 0.5024 (tt0) cc_final: 0.4439 (tp30) REVERT: B 262 GLN cc_start: 0.7473 (mt0) cc_final: 0.7130 (mt0) REVERT: B 263 TYR cc_start: 0.8313 (t80) cc_final: 0.7692 (t80) REVERT: B 305 LYS cc_start: 0.8604 (ptpp) cc_final: 0.8141 (ptpp) REVERT: B 311 VAL cc_start: 0.7419 (t) cc_final: 0.7146 (p) REVERT: C 38 MET cc_start: 0.8214 (mmt) cc_final: 0.7783 (mmt) REVERT: C 50 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8393 (tp-100) REVERT: C 68 ASN cc_start: 0.8221 (p0) cc_final: 0.7961 (p0) REVERT: C 85 PHE cc_start: 0.6789 (p90) cc_final: 0.6217 (p90) REVERT: C 114 MET cc_start: 0.7178 (mmm) cc_final: 0.6340 (mtm) REVERT: C 160 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8453 (ttmt) REVERT: C 207 ASN cc_start: 0.8001 (t0) cc_final: 0.7688 (m-40) REVERT: C 316 ASN cc_start: 0.7513 (t0) cc_final: 0.7254 (t0) REVERT: D 205 MET cc_start: 0.2827 (mtm) cc_final: 0.2245 (mtm) REVERT: E 142 ARG cc_start: 0.4230 (mtp85) cc_final: 0.3630 (mtp85) REVERT: F 103 LEU cc_start: 0.7816 (mm) cc_final: 0.7615 (mm) REVERT: F 135 GLU cc_start: 0.7976 (mp0) cc_final: 0.7710 (mp0) REVERT: F 152 TYR cc_start: 0.8339 (m-80) cc_final: 0.7890 (m-80) REVERT: F 154 VAL cc_start: 0.8093 (t) cc_final: 0.7753 (t) REVERT: F 261 ILE cc_start: 0.5076 (pt) cc_final: 0.4693 (tp) REVERT: F 264 GLN cc_start: 0.7232 (pp30) cc_final: 0.6718 (pp30) REVERT: F 345 LEU cc_start: 0.7046 (tt) cc_final: 0.5917 (pp) REVERT: F 384 ARG cc_start: 0.2671 (OUTLIER) cc_final: 0.2202 (ptp-170) REVERT: F 487 ARG cc_start: 0.6791 (mtt-85) cc_final: 0.6521 (mtt90) REVERT: F 523 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8133 (pp) REVERT: F 548 ASP cc_start: 0.6011 (m-30) cc_final: 0.5704 (t0) REVERT: F 565 ILE cc_start: 0.3892 (mp) cc_final: 0.2973 (mp) REVERT: F 592 TYR cc_start: 0.6823 (t80) cc_final: 0.6400 (t80) outliers start: 5 outliers final: 2 residues processed: 469 average time/residue: 0.7129 time to fit residues: 490.3668 Evaluate side-chains 444 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 440 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.0060 chunk 67 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN B 52 ASN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 375 GLN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 GLN F 521 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18960 Z= 0.168 Angle : 0.552 7.768 25744 Z= 0.308 Chirality : 0.045 0.169 2697 Planarity : 0.004 0.060 3458 Dihedral : 4.992 29.995 2678 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2401 helix: 1.15 (0.32), residues: 234 sheet: -0.14 (0.15), residues: 1077 loop : -0.91 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 418 HIS 0.008 0.001 HIS A 21 PHE 0.017 0.002 PHE F 514 TYR 0.028 0.002 TYR C 313 ARG 0.005 0.000 ARG F 460 *********************** 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 448 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 447 time to evaluate : 2.565 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: A 16 LYS cc_start: 0.8466 (pttt) cc_final: 0.8238 (pttt) REVERT: A 38 MET cc_start: 0.8305 (mmt) cc_final: 0.7679 (mmt) REVERT: A 65 PHE cc_start: 0.6849 (m-80) cc_final: 0.6301 (m-80) REVERT: A 85 PHE cc_start: 0.7159 (p90) cc_final: 0.6325 (p90) REVERT: A 90 TYR cc_start: 0.7451 (t80) cc_final: 0.6844 (t80) REVERT: A 92 ASP cc_start: 0.8565 (p0) cc_final: 0.8012 (p0) REVERT: A 101 ASN cc_start: 0.7691 (t0) cc_final: 0.7443 (t0) REVERT: A 121 ASP cc_start: 0.8217 (m-30) cc_final: 0.7846 (m-30) REVERT: A 129 PHE cc_start: 0.6593 (m-80) cc_final: 0.6160 (m-80) REVERT: A 258 LEU cc_start: 0.7076 (mm) cc_final: 0.6796 (mm) REVERT: A 281 LYS cc_start: 0.8829 (mttp) cc_final: 0.8318 (mttp) REVERT: A 307 MET cc_start: 0.7822 (tpp) cc_final: 0.7522 (tpp) REVERT: A 310 TYR cc_start: 0.7453 (p90) cc_final: 0.6956 (p90) REVERT: B 16 LYS cc_start: 0.7996 (pttt) cc_final: 0.7739 (pttt) REVERT: B 46 LYS cc_start: 0.7540 (mtpt) cc_final: 0.7161 (mtpt) REVERT: B 65 PHE cc_start: 0.7937 (m-80) cc_final: 0.7733 (m-80) REVERT: B 66 GLN cc_start: 0.7090 (mm110) cc_final: 0.6509 (mm110) REVERT: B 79 ASN cc_start: 0.7814 (m-40) cc_final: 0.7446 (m-40) REVERT: B 109 LEU cc_start: 0.7946 (mt) cc_final: 0.7740 (mt) REVERT: B 124 TYR cc_start: 0.7403 (m-80) cc_final: 0.7062 (m-80) REVERT: B 164 ASP cc_start: 0.7890 (p0) cc_final: 0.7523 (p0) REVERT: B 183 GLU cc_start: 0.8217 (tt0) cc_final: 0.7166 (mt-10) REVERT: B 201 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8245 (mt-10) REVERT: B 219 LYS cc_start: 0.7478 (pttt) cc_final: 0.7034 (pttt) REVERT: B 224 ASN cc_start: 0.8844 (m-40) cc_final: 0.8425 (m-40) REVERT: B 262 GLN cc_start: 0.7414 (mt0) cc_final: 0.7103 (mt0) REVERT: B 263 TYR cc_start: 0.8081 (t80) cc_final: 0.7514 (t80) REVERT: B 295 PHE cc_start: 0.6966 (m-10) cc_final: 0.6723 (m-10) REVERT: B 305 LYS cc_start: 0.8496 (ptpp) cc_final: 0.7968 (ptpp) REVERT: B 311 VAL cc_start: 0.7475 (t) cc_final: 0.7207 (p) REVERT: C 38 MET cc_start: 0.8137 (mmt) cc_final: 0.7488 (mmt) REVERT: C 43 LEU cc_start: 0.8285 (tp) cc_final: 0.8078 (tp) REVERT: C 49 THR cc_start: 0.8116 (t) cc_final: 0.7881 (t) REVERT: C 54 ASP cc_start: 0.6959 (m-30) cc_final: 0.6753 (m-30) REVERT: C 85 PHE cc_start: 0.6647 (p90) cc_final: 0.6152 (p90) REVERT: C 114 MET cc_start: 0.6999 (mmm) cc_final: 0.6394 (mtm) REVERT: C 303 PHE cc_start: 0.7092 (m-80) cc_final: 0.6812 (m-80) REVERT: D 205 MET cc_start: 0.2706 (mtm) cc_final: 0.2159 (mtm) REVERT: E 142 ARG cc_start: 0.4485 (mtp85) cc_final: 0.3932 (mtp85) REVERT: F 135 GLU cc_start: 0.7895 (mp0) cc_final: 0.7571 (mp0) REVERT: F 151 ASN cc_start: 0.7908 (t0) cc_final: 0.7661 (p0) REVERT: F 345 LEU cc_start: 0.7020 (tt) cc_final: 0.5948 (pp) REVERT: F 548 ASP cc_start: 0.5908 (m-30) cc_final: 0.5435 (t0) REVERT: F 565 ILE cc_start: 0.3584 (mp) cc_final: 0.2863 (mp) REVERT: F 592 TYR cc_start: 0.6463 (t80) cc_final: 0.5993 (t80) outliers start: 1 outliers final: 0 residues processed: 447 average time/residue: 0.7376 time to fit residues: 484.8423 Evaluate side-chains 425 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 30.0000 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 50.0000 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5483 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 18960 Z= 0.380 Angle : 0.721 9.516 25744 Z= 0.407 Chirality : 0.046 0.196 2697 Planarity : 0.006 0.069 3458 Dihedral : 5.541 31.810 2678 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 27.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 0.37 % Allowed : 2.41 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2401 helix: 0.29 (0.31), residues: 258 sheet: -0.41 (0.15), residues: 1109 loop : -1.36 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 61 HIS 0.012 0.002 HIS E 146 PHE 0.030 0.002 PHE D 376 TYR 0.029 0.003 TYR B 90 ARG 0.016 0.001 ARG F 526 *********************** 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 465 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 460 time to evaluate : 2.721 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: A 13 LEU cc_start: 0.8362 (tp) cc_final: 0.8128 (tp) REVERT: A 38 MET cc_start: 0.8377 (mmt) cc_final: 0.8025 (mmm) REVERT: A 65 PHE cc_start: 0.6903 (m-80) cc_final: 0.6619 (m-80) REVERT: A 90 TYR cc_start: 0.7654 (t80) cc_final: 0.7089 (t80) REVERT: A 114 MET cc_start: 0.6425 (mmt) cc_final: 0.6189 (mmt) REVERT: A 115 LEU cc_start: 0.8285 (mm) cc_final: 0.8049 (mm) REVERT: A 129 PHE cc_start: 0.6849 (m-80) cc_final: 0.6446 (m-80) REVERT: A 181 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 258 LEU cc_start: 0.7200 (mm) cc_final: 0.6938 (mm) REVERT: A 267 PHE cc_start: 0.8362 (p90) cc_final: 0.8015 (p90) REVERT: A 303 PHE cc_start: 0.8473 (m-80) cc_final: 0.7632 (m-80) REVERT: A 307 MET cc_start: 0.7723 (tpp) cc_final: 0.7241 (tpp) REVERT: A 310 TYR cc_start: 0.7539 (p90) cc_final: 0.6841 (p90) REVERT: B 4 TYR cc_start: 0.7831 (t80) cc_final: 0.7423 (t80) REVERT: B 6 LYS cc_start: 0.8361 (ttpp) cc_final: 0.8043 (ttpt) REVERT: B 16 LYS cc_start: 0.8066 (pttt) cc_final: 0.7820 (pttt) REVERT: B 40 TYR cc_start: 0.7919 (p90) cc_final: 0.7057 (p90) REVERT: B 97 ASP cc_start: 0.8294 (p0) cc_final: 0.7995 (p0) REVERT: B 109 LEU cc_start: 0.8127 (mt) cc_final: 0.7897 (mt) REVERT: B 114 MET cc_start: 0.7905 (tpt) cc_final: 0.7621 (tpt) REVERT: B 156 GLN cc_start: 0.7200 (tt0) cc_final: 0.6934 (tt0) REVERT: B 183 GLU cc_start: 0.8317 (tt0) cc_final: 0.7319 (mt-10) REVERT: B 201 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 219 LYS cc_start: 0.7671 (pttt) cc_final: 0.7168 (pttt) REVERT: B 224 ASN cc_start: 0.8775 (m-40) cc_final: 0.8310 (m-40) REVERT: B 262 GLN cc_start: 0.7615 (mt0) cc_final: 0.7165 (mt0) REVERT: B 263 TYR cc_start: 0.8282 (t80) cc_final: 0.7992 (t80) REVERT: B 305 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8192 (ptpp) REVERT: C 7 ASP cc_start: 0.8039 (m-30) cc_final: 0.7827 (m-30) REVERT: C 32 TYR cc_start: 0.7416 (t80) cc_final: 0.6999 (t80) REVERT: C 49 THR cc_start: 0.8269 (t) cc_final: 0.8032 (t) REVERT: C 54 ASP cc_start: 0.7082 (m-30) cc_final: 0.6856 (m-30) REVERT: C 85 PHE cc_start: 0.6693 (p90) cc_final: 0.6323 (p90) REVERT: C 114 MET cc_start: 0.7549 (mmm) cc_final: 0.6962 (mtm) REVERT: C 160 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8781 (ttmt) REVERT: C 207 ASN cc_start: 0.8061 (t0) cc_final: 0.7748 (p0) REVERT: C 303 PHE cc_start: 0.7114 (m-80) cc_final: 0.6810 (m-80) REVERT: C 319 ASP cc_start: 0.7835 (p0) cc_final: 0.7470 (p0) REVERT: C 321 ASP cc_start: 0.6462 (p0) cc_final: 0.6055 (p0) REVERT: D 205 MET cc_start: 0.3406 (mtm) cc_final: 0.2775 (mtm) REVERT: E 142 ARG cc_start: 0.4037 (mtp85) cc_final: 0.3293 (mtp85) REVERT: E 203 MET cc_start: 0.2381 (mtt) cc_final: 0.2167 (mtt) REVERT: F 135 GLU cc_start: 0.8086 (mp0) cc_final: 0.7694 (mp0) REVERT: F 152 TYR cc_start: 0.8330 (m-80) cc_final: 0.8047 (m-80) REVERT: F 159 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6068 (pp30) REVERT: F 166 VAL cc_start: 0.7027 (m) cc_final: 0.6773 (p) REVERT: F 295 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7599 (tm-30) REVERT: F 306 VAL cc_start: 0.8704 (t) cc_final: 0.8413 (m) REVERT: F 345 LEU cc_start: 0.7467 (tt) cc_final: 0.6137 (pp) REVERT: F 346 GLN cc_start: 0.6577 (tp-100) cc_final: 0.6264 (tp-100) REVERT: F 548 ASP cc_start: 0.6273 (m-30) cc_final: 0.5703 (t0) REVERT: F 565 ILE cc_start: 0.3712 (mp) cc_final: 0.2901 (mp) REVERT: F 592 TYR cc_start: 0.6789 (t80) cc_final: 0.6302 (t80) outliers start: 5 outliers final: 1 residues processed: 465 average time/residue: 0.7382 time to fit residues: 508.2030 Evaluate side-chains 442 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 440 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 40.0000 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** B 52 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 18960 Z= 0.395 Angle : 0.717 9.288 25744 Z= 0.407 Chirality : 0.047 0.208 2697 Planarity : 0.006 0.091 3458 Dihedral : 5.708 34.770 2678 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.26 % Allowed : 2.30 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2401 helix: 0.07 (0.31), residues: 252 sheet: -0.48 (0.15), residues: 1124 loop : -1.49 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 61 HIS 0.013 0.002 HIS E 146 PHE 0.029 0.002 PHE D 376 TYR 0.061 0.003 TYR B 313 ARG 0.008 0.001 ARG F 384 *********************** 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 472 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 469 time to evaluate : 2.616 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: A 13 LEU cc_start: 0.8357 (tp) cc_final: 0.8113 (tp) REVERT: A 16 LYS cc_start: 0.8607 (pttt) cc_final: 0.8360 (pttt) REVERT: A 65 PHE cc_start: 0.7219 (m-10) cc_final: 0.6949 (m-10) REVERT: A 90 TYR cc_start: 0.7501 (t80) cc_final: 0.7035 (t80) REVERT: A 114 MET cc_start: 0.6523 (mmt) cc_final: 0.6307 (mmt) REVERT: A 115 LEU cc_start: 0.8327 (mm) cc_final: 0.8086 (mm) REVERT: A 128 PHE cc_start: 0.7265 (m-80) cc_final: 0.6603 (m-80) REVERT: A 161 ASN cc_start: 0.8921 (t0) cc_final: 0.8676 (t0) REVERT: A 267 PHE cc_start: 0.8558 (p90) cc_final: 0.8162 (p90) REVERT: A 303 PHE cc_start: 0.8546 (m-80) cc_final: 0.7723 (m-80) REVERT: A 307 MET cc_start: 0.7657 (tpp) cc_final: 0.7267 (tpp) REVERT: A 310 TYR cc_start: 0.7548 (p90) cc_final: 0.6745 (p90) REVERT: A 318 ILE cc_start: 0.8737 (mm) cc_final: 0.8409 (mp) REVERT: B 4 TYR cc_start: 0.7981 (t80) cc_final: 0.7363 (t80) REVERT: B 16 LYS cc_start: 0.8048 (pttt) cc_final: 0.7690 (pttt) REVERT: B 40 TYR cc_start: 0.7992 (p90) cc_final: 0.7158 (p90) REVERT: B 80 LYS cc_start: 0.8954 (ptpp) cc_final: 0.8473 (ptpp) REVERT: B 97 ASP cc_start: 0.8260 (p0) cc_final: 0.8022 (p0) REVERT: B 109 LEU cc_start: 0.8344 (mt) cc_final: 0.8104 (mt) REVERT: B 114 MET cc_start: 0.7981 (tpt) cc_final: 0.7714 (tpt) REVERT: B 183 GLU cc_start: 0.8294 (tt0) cc_final: 0.7274 (mt-10) REVERT: B 201 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8306 (mt-10) REVERT: B 219 LYS cc_start: 0.7686 (pttt) cc_final: 0.7197 (pttt) REVERT: B 262 GLN cc_start: 0.7738 (mt0) cc_final: 0.7344 (mt0) REVERT: B 295 PHE cc_start: 0.6979 (m-10) cc_final: 0.6733 (m-10) REVERT: C 32 TYR cc_start: 0.7367 (t80) cc_final: 0.6978 (t80) REVERT: C 49 THR cc_start: 0.8018 (t) cc_final: 0.7818 (t) REVERT: C 85 PHE cc_start: 0.6653 (p90) cc_final: 0.6427 (p90) REVERT: C 89 LYS cc_start: 0.8179 (tttt) cc_final: 0.7918 (tttt) REVERT: C 114 MET cc_start: 0.7635 (mmm) cc_final: 0.7188 (mtm) REVERT: C 160 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8789 (ttmt) REVERT: C 207 ASN cc_start: 0.8317 (t0) cc_final: 0.7900 (p0) REVERT: C 303 PHE cc_start: 0.7144 (m-80) cc_final: 0.6831 (m-80) REVERT: C 319 ASP cc_start: 0.7603 (p0) cc_final: 0.7239 (p0) REVERT: C 321 ASP cc_start: 0.6159 (p0) cc_final: 0.5833 (p0) REVERT: D 205 MET cc_start: 0.3608 (mtm) cc_final: 0.2889 (mtm) REVERT: E 142 ARG cc_start: 0.4012 (mtp85) cc_final: 0.3298 (mtp85) REVERT: F 166 VAL cc_start: 0.7211 (m) cc_final: 0.6850 (p) REVERT: F 268 SER cc_start: 0.7843 (t) cc_final: 0.7423 (t) REVERT: F 295 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7719 (tm-30) REVERT: F 305 ILE cc_start: 0.7177 (mt) cc_final: 0.6961 (mt) REVERT: F 306 VAL cc_start: 0.8794 (t) cc_final: 0.8408 (m) REVERT: F 345 LEU cc_start: 0.7748 (tt) cc_final: 0.6659 (pp) REVERT: F 346 GLN cc_start: 0.6817 (tp-100) cc_final: 0.6251 (tp-100) REVERT: F 397 ASN cc_start: 0.4026 (p0) cc_final: 0.3605 (p0) REVERT: F 445 ASP cc_start: 0.5750 (OUTLIER) cc_final: -0.0023 (t70) REVERT: F 548 ASP cc_start: 0.6226 (m-30) cc_final: 0.5762 (t0) REVERT: F 565 ILE cc_start: 0.4055 (mp) cc_final: 0.3040 (mp) outliers start: 3 outliers final: 0 residues processed: 471 average time/residue: 0.7394 time to fit residues: 510.6955 Evaluate side-chains 439 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 0.0980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18960 Z= 0.209 Angle : 0.576 7.291 25744 Z= 0.323 Chirality : 0.045 0.173 2697 Planarity : 0.005 0.073 3458 Dihedral : 5.268 30.351 2678 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.10 % Allowed : 1.20 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2401 helix: 1.19 (0.33), residues: 234 sheet: -0.32 (0.15), residues: 1109 loop : -1.21 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 547 HIS 0.007 0.001 HIS E 146 PHE 0.024 0.002 PHE F 594 TYR 0.031 0.002 TYR B 313 ARG 0.010 0.001 ARG D 258 *********************** 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 457 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 2.640 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 13 LEU cc_start: 0.8301 (tp) cc_final: 0.8056 (tp) REVERT: A 16 LYS cc_start: 0.8536 (pttt) cc_final: 0.8332 (pttt) REVERT: A 85 PHE cc_start: 0.6764 (p90) cc_final: 0.6123 (p90) REVERT: A 90 TYR cc_start: 0.7380 (t80) cc_final: 0.7042 (t80) REVERT: A 115 LEU cc_start: 0.8359 (mm) cc_final: 0.8123 (mm) REVERT: A 128 PHE cc_start: 0.7247 (m-80) cc_final: 0.6576 (m-80) REVERT: A 161 ASN cc_start: 0.8810 (t0) cc_final: 0.8566 (t0) REVERT: A 201 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7710 (mt-10) REVERT: A 267 PHE cc_start: 0.8476 (p90) cc_final: 0.8124 (p90) REVERT: A 303 PHE cc_start: 0.8455 (m-80) cc_final: 0.7698 (m-80) REVERT: A 307 MET cc_start: 0.7677 (tpp) cc_final: 0.7324 (tpp) REVERT: B 4 TYR cc_start: 0.7885 (t80) cc_final: 0.7508 (t80) REVERT: B 6 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8148 (ttpt) REVERT: B 16 LYS cc_start: 0.8077 (pttt) cc_final: 0.7687 (pttt) REVERT: B 40 TYR cc_start: 0.7942 (p90) cc_final: 0.7269 (p90) REVERT: B 80 LYS cc_start: 0.8947 (ptpp) cc_final: 0.8450 (ptpp) REVERT: B 97 ASP cc_start: 0.8085 (p0) cc_final: 0.7809 (p0) REVERT: B 114 MET cc_start: 0.7840 (tpt) cc_final: 0.7599 (tpt) REVERT: B 183 GLU cc_start: 0.8305 (tt0) cc_final: 0.7549 (mt-10) REVERT: B 201 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 219 LYS cc_start: 0.7575 (pttt) cc_final: 0.7087 (pttt) REVERT: B 262 GLN cc_start: 0.7675 (mt0) cc_final: 0.7246 (mt0) REVERT: B 263 TYR cc_start: 0.8269 (t80) cc_final: 0.7852 (t80) REVERT: B 295 PHE cc_start: 0.6968 (m-10) cc_final: 0.6735 (m-10) REVERT: C 32 TYR cc_start: 0.7331 (t80) cc_final: 0.6976 (t80) REVERT: C 54 ASP cc_start: 0.7096 (m-30) cc_final: 0.6879 (m-30) REVERT: C 85 PHE cc_start: 0.6645 (p90) cc_final: 0.6369 (p90) REVERT: C 89 LYS cc_start: 0.8069 (tttt) cc_final: 0.7796 (tttt) REVERT: C 114 MET cc_start: 0.7565 (mmm) cc_final: 0.7113 (mtm) REVERT: C 149 ASP cc_start: 0.8893 (m-30) cc_final: 0.8630 (m-30) REVERT: C 160 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8662 (ttmt) REVERT: C 207 ASN cc_start: 0.8238 (t0) cc_final: 0.7808 (p0) REVERT: C 282 ASP cc_start: 0.6989 (m-30) cc_final: 0.6705 (m-30) REVERT: C 303 PHE cc_start: 0.7136 (m-80) cc_final: 0.6872 (m-80) REVERT: C 319 ASP cc_start: 0.7718 (p0) cc_final: 0.7358 (p0) REVERT: C 321 ASP cc_start: 0.6215 (p0) cc_final: 0.5881 (p0) REVERT: D 205 MET cc_start: 0.3676 (mtm) cc_final: 0.2968 (mtm) REVERT: E 142 ARG cc_start: 0.3879 (mtp85) cc_final: 0.3195 (mtp85) REVERT: E 348 MET cc_start: -0.1116 (pmm) cc_final: -0.2021 (pmm) REVERT: F 151 ASN cc_start: 0.7743 (t0) cc_final: 0.7530 (p0) REVERT: F 166 VAL cc_start: 0.7177 (m) cc_final: 0.6846 (p) REVERT: F 202 LEU cc_start: 0.8184 (mm) cc_final: 0.7984 (mm) REVERT: F 268 SER cc_start: 0.7846 (t) cc_final: 0.7456 (t) REVERT: F 295 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7706 (tm-30) REVERT: F 305 ILE cc_start: 0.6996 (mt) cc_final: 0.6218 (mt) REVERT: F 345 LEU cc_start: 0.7643 (tt) cc_final: 0.6515 (pp) REVERT: F 346 GLN cc_start: 0.6620 (tp-100) cc_final: 0.6109 (tp-100) REVERT: F 397 ASN cc_start: 0.4066 (p0) cc_final: 0.3654 (p0) REVERT: F 548 ASP cc_start: 0.5992 (m-30) cc_final: 0.5575 (t0) REVERT: F 565 ILE cc_start: 0.3821 (mp) cc_final: 0.3189 (mp) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.7219 time to fit residues: 482.6526 Evaluate side-chains 428 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 169 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 50.0000 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS E 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18960 Z= 0.167 Angle : 0.547 6.548 25744 Z= 0.302 Chirality : 0.045 0.184 2697 Planarity : 0.004 0.098 3458 Dihedral : 4.990 31.097 2678 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.10 % Allowed : 0.84 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2401 helix: 1.75 (0.34), residues: 232 sheet: -0.27 (0.15), residues: 1119 loop : -0.99 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 61 HIS 0.005 0.001 HIS F 208 PHE 0.034 0.002 PHE A 118 TYR 0.030 0.001 TYR C 63 ARG 0.017 0.001 ARG F 526 *********************** 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 451 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 2.725 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 13 LEU cc_start: 0.8239 (tp) cc_final: 0.8022 (tp) REVERT: A 16 LYS cc_start: 0.8495 (pttt) cc_final: 0.8265 (pttt) REVERT: A 79 ASN cc_start: 0.7526 (m110) cc_final: 0.7288 (m110) REVERT: A 90 TYR cc_start: 0.7311 (t80) cc_final: 0.7042 (t80) REVERT: A 115 LEU cc_start: 0.8225 (mm) cc_final: 0.7999 (mm) REVERT: A 128 PHE cc_start: 0.7231 (m-80) cc_final: 0.6546 (m-80) REVERT: A 161 ASN cc_start: 0.8810 (t0) cc_final: 0.8432 (t0) REVERT: A 201 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 258 LEU cc_start: 0.7236 (mm) cc_final: 0.6908 (mm) REVERT: A 267 PHE cc_start: 0.8433 (p90) cc_final: 0.8035 (p90) REVERT: A 303 PHE cc_start: 0.8446 (m-80) cc_final: 0.7688 (m-80) REVERT: A 307 MET cc_start: 0.7643 (tpp) cc_final: 0.7331 (tpp) REVERT: B 4 TYR cc_start: 0.7796 (t80) cc_final: 0.6833 (t80) REVERT: B 6 LYS cc_start: 0.8422 (ttpp) cc_final: 0.7968 (ttpt) REVERT: B 40 TYR cc_start: 0.8028 (p90) cc_final: 0.7547 (p90) REVERT: B 66 GLN cc_start: 0.7251 (mm110) cc_final: 0.6625 (mm110) REVERT: B 76 GLN cc_start: 0.8507 (mp10) cc_final: 0.8255 (mp10) REVERT: B 80 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8360 (ptpp) REVERT: B 97 ASP cc_start: 0.7896 (p0) cc_final: 0.7425 (p0) REVERT: B 109 LEU cc_start: 0.8079 (mt) cc_final: 0.7825 (mt) REVERT: B 121 ASP cc_start: 0.7551 (m-30) cc_final: 0.7141 (m-30) REVERT: B 183 GLU cc_start: 0.8221 (tt0) cc_final: 0.7491 (mt-10) REVERT: B 201 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8263 (mt-10) REVERT: B 219 LYS cc_start: 0.7567 (pttt) cc_final: 0.7090 (pttt) REVERT: B 225 ILE cc_start: 0.7493 (mt) cc_final: 0.7224 (mt) REVERT: B 262 GLN cc_start: 0.7606 (mt0) cc_final: 0.7329 (mt0) REVERT: B 263 TYR cc_start: 0.8179 (t80) cc_final: 0.7872 (t80) REVERT: B 269 LEU cc_start: 0.8161 (tp) cc_final: 0.7913 (tp) REVERT: B 295 PHE cc_start: 0.6962 (m-10) cc_final: 0.6730 (m-10) REVERT: B 306 ASN cc_start: 0.8470 (m110) cc_final: 0.8259 (m-40) REVERT: C 7 ASP cc_start: 0.7868 (m-30) cc_final: 0.7628 (m-30) REVERT: C 49 THR cc_start: 0.7851 (t) cc_final: 0.7527 (t) REVERT: C 85 PHE cc_start: 0.6639 (p90) cc_final: 0.6332 (p90) REVERT: C 89 LYS cc_start: 0.7995 (tttt) cc_final: 0.7729 (tttt) REVERT: C 114 MET cc_start: 0.7498 (mmm) cc_final: 0.7067 (mtm) REVERT: C 207 ASN cc_start: 0.8208 (t0) cc_final: 0.7795 (p0) REVERT: C 247 THR cc_start: 0.8107 (p) cc_final: 0.7787 (p) REVERT: C 282 ASP cc_start: 0.7012 (m-30) cc_final: 0.6722 (m-30) REVERT: C 303 PHE cc_start: 0.7068 (m-80) cc_final: 0.6833 (m-80) REVERT: C 316 ASN cc_start: 0.7720 (t0) cc_final: 0.7432 (t0) REVERT: C 319 ASP cc_start: 0.7665 (p0) cc_final: 0.7294 (p0) REVERT: C 321 ASP cc_start: 0.6313 (p0) cc_final: 0.6014 (p0) REVERT: D 205 MET cc_start: 0.3695 (mtm) cc_final: 0.2983 (mtm) REVERT: E 142 ARG cc_start: 0.3838 (mtp85) cc_final: 0.3218 (mtp85) REVERT: E 348 MET cc_start: -0.1297 (pmm) cc_final: -0.2118 (pmm) REVERT: F 108 GLU cc_start: 0.6944 (mp0) cc_final: 0.6672 (mp0) REVERT: F 166 VAL cc_start: 0.7153 (m) cc_final: 0.6821 (p) REVERT: F 202 LEU cc_start: 0.8149 (mm) cc_final: 0.7919 (mm) REVERT: F 345 LEU cc_start: 0.7645 (tt) cc_final: 0.6549 (pp) REVERT: F 346 GLN cc_start: 0.6403 (tp-100) cc_final: 0.6062 (tp-100) REVERT: F 354 GLU cc_start: 0.4058 (pp20) cc_final: 0.3717 (pp20) REVERT: F 397 ASN cc_start: 0.4087 (p0) cc_final: 0.3666 (p0) REVERT: F 548 ASP cc_start: 0.5951 (m-30) cc_final: 0.5573 (t0) REVERT: F 565 ILE cc_start: 0.3530 (mp) cc_final: 0.2943 (mp) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.7252 time to fit residues: 476.9524 Evaluate side-chains 427 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 114 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 18960 Z= 0.429 Angle : 0.740 9.248 25744 Z= 0.420 Chirality : 0.047 0.172 2697 Planarity : 0.006 0.063 3458 Dihedral : 5.750 38.978 2678 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 31.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.99 % Favored : 91.97 % Rotamer: Outliers : 0.10 % Allowed : 1.15 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2401 helix: 0.27 (0.31), residues: 253 sheet: -0.62 (0.15), residues: 1111 loop : -1.49 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 61 HIS 0.009 0.002 HIS C 21 PHE 0.030 0.003 PHE B 65 TYR 0.037 0.003 TYR E 216 ARG 0.010 0.001 ARG F 384 *********************** 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 456 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.896 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8402 (tp) cc_final: 0.8152 (tp) REVERT: A 38 MET cc_start: 0.8440 (mmt) cc_final: 0.8127 (mmm) REVERT: A 65 PHE cc_start: 0.7328 (m-10) cc_final: 0.7124 (m-10) REVERT: A 90 TYR cc_start: 0.7350 (t80) cc_final: 0.7028 (t80) REVERT: A 98 TYR cc_start: 0.8092 (t80) cc_final: 0.7566 (t80) REVERT: A 101 ASN cc_start: 0.8045 (t0) cc_final: 0.7724 (t0) REVERT: A 128 PHE cc_start: 0.7335 (m-80) cc_final: 0.6669 (m-80) REVERT: A 161 ASN cc_start: 0.8871 (t0) cc_final: 0.8504 (t0) REVERT: A 198 ASN cc_start: 0.8944 (m-40) cc_final: 0.8405 (m110) REVERT: A 258 LEU cc_start: 0.7284 (mm) cc_final: 0.7030 (mm) REVERT: A 267 PHE cc_start: 0.8704 (p90) cc_final: 0.8331 (p90) REVERT: A 303 PHE cc_start: 0.8611 (m-80) cc_final: 0.8133 (m-80) REVERT: B 4 TYR cc_start: 0.8099 (t80) cc_final: 0.7727 (t80) REVERT: B 6 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8182 (ttpt) REVERT: B 40 TYR cc_start: 0.8041 (p90) cc_final: 0.7318 (p90) REVERT: B 62 GLU cc_start: 0.7958 (tt0) cc_final: 0.7529 (tt0) REVERT: B 109 LEU cc_start: 0.8356 (mt) cc_final: 0.8090 (mt) REVERT: B 114 MET cc_start: 0.8058 (tpt) cc_final: 0.7849 (tpt) REVERT: B 121 ASP cc_start: 0.7635 (m-30) cc_final: 0.7435 (m-30) REVERT: B 124 TYR cc_start: 0.7667 (m-80) cc_final: 0.7254 (m-80) REVERT: B 126 ASP cc_start: 0.7541 (m-30) cc_final: 0.7148 (m-30) REVERT: B 183 GLU cc_start: 0.8517 (tt0) cc_final: 0.7811 (mt-10) REVERT: B 201 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8306 (mt-10) REVERT: B 219 LYS cc_start: 0.7732 (pttt) cc_final: 0.7220 (pttt) REVERT: B 263 TYR cc_start: 0.8234 (t80) cc_final: 0.7934 (t80) REVERT: B 295 PHE cc_start: 0.7043 (m-10) cc_final: 0.6821 (m-10) REVERT: B 310 TYR cc_start: 0.7099 (p90) cc_final: 0.6787 (p90) REVERT: C 32 TYR cc_start: 0.7338 (t80) cc_final: 0.6906 (t80) REVERT: C 85 PHE cc_start: 0.6686 (p90) cc_final: 0.6447 (p90) REVERT: C 89 LYS cc_start: 0.8315 (tttt) cc_final: 0.8014 (tttt) REVERT: C 114 MET cc_start: 0.7684 (mmm) cc_final: 0.7346 (mtm) REVERT: C 149 ASP cc_start: 0.9032 (m-30) cc_final: 0.8801 (m-30) REVERT: C 160 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8630 (ttmt) REVERT: C 207 ASN cc_start: 0.8348 (t0) cc_final: 0.7940 (p0) REVERT: C 247 THR cc_start: 0.8360 (p) cc_final: 0.7974 (p) REVERT: C 282 ASP cc_start: 0.6795 (m-30) cc_final: 0.6594 (m-30) REVERT: C 303 PHE cc_start: 0.7232 (m-80) cc_final: 0.6951 (m-80) REVERT: C 319 ASP cc_start: 0.7701 (p0) cc_final: 0.7338 (p0) REVERT: C 321 ASP cc_start: 0.6233 (p0) cc_final: 0.5848 (p0) REVERT: D 205 MET cc_start: 0.4079 (mtm) cc_final: 0.3368 (mtm) REVERT: E 346 MET cc_start: 0.1702 (ptt) cc_final: 0.1472 (ptt) REVERT: E 348 MET cc_start: -0.0894 (pmm) cc_final: -0.1665 (pmm) REVERT: F 166 VAL cc_start: 0.7369 (m) cc_final: 0.7120 (p) REVERT: F 299 GLN cc_start: 0.8525 (mp-120) cc_final: 0.8288 (mp-120) REVERT: F 305 ILE cc_start: 0.7162 (mt) cc_final: 0.6882 (mt) REVERT: F 346 GLN cc_start: 0.6983 (tp-100) cc_final: 0.6670 (tp-100) REVERT: F 397 ASN cc_start: 0.4441 (p0) cc_final: 0.4065 (p0) REVERT: F 548 ASP cc_start: 0.5962 (m-30) cc_final: 0.5682 (t0) REVERT: F 565 ILE cc_start: 0.4040 (mp) cc_final: 0.3143 (mp) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.7123 time to fit residues: 476.0893 Evaluate side-chains 440 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 52 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 18960 Z= 0.352 Angle : 0.686 9.342 25744 Z= 0.388 Chirality : 0.046 0.165 2697 Planarity : 0.005 0.081 3458 Dihedral : 5.765 37.828 2678 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.16 % Allowed : 0.47 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2401 helix: 0.34 (0.32), residues: 250 sheet: -0.57 (0.15), residues: 1089 loop : -1.62 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 61 HIS 0.009 0.002 HIS F 368 PHE 0.040 0.002 PHE A 118 TYR 0.046 0.002 TYR A 124 ARG 0.010 0.001 ARG D 328 *********************** 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 463 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 462 time to evaluate : 2.682 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8348 (tp) cc_final: 0.8112 (tp) REVERT: A 38 MET cc_start: 0.8371 (mmt) cc_final: 0.8047 (mmm) REVERT: A 65 PHE cc_start: 0.7365 (m-10) cc_final: 0.7138 (m-10) REVERT: A 113 ASP cc_start: 0.8047 (t0) cc_final: 0.7530 (t0) REVERT: A 128 PHE cc_start: 0.7318 (m-80) cc_final: 0.6610 (m-80) REVERT: A 161 ASN cc_start: 0.8767 (t0) cc_final: 0.8482 (t0) REVERT: A 180 TYR cc_start: 0.8112 (t80) cc_final: 0.7802 (t80) REVERT: A 258 LEU cc_start: 0.7313 (mm) cc_final: 0.7010 (mm) REVERT: A 267 PHE cc_start: 0.8687 (p90) cc_final: 0.8309 (p90) REVERT: A 293 ASN cc_start: 0.7619 (m-40) cc_final: 0.7096 (t0) REVERT: A 303 PHE cc_start: 0.8665 (m-80) cc_final: 0.8149 (m-80) REVERT: B 4 TYR cc_start: 0.8050 (t80) cc_final: 0.7648 (t80) REVERT: B 6 LYS cc_start: 0.8419 (ttpp) cc_final: 0.8106 (ttpt) REVERT: B 40 TYR cc_start: 0.8092 (p90) cc_final: 0.7467 (p90) REVERT: B 65 PHE cc_start: 0.8226 (m-10) cc_final: 0.7770 (m-10) REVERT: B 76 GLN cc_start: 0.8561 (mp10) cc_final: 0.8271 (mp10) REVERT: B 109 LEU cc_start: 0.8365 (mt) cc_final: 0.8085 (mt) REVERT: B 114 MET cc_start: 0.8026 (tpt) cc_final: 0.7809 (tpt) REVERT: B 124 TYR cc_start: 0.7666 (m-80) cc_final: 0.7286 (m-80) REVERT: B 183 GLU cc_start: 0.8439 (tt0) cc_final: 0.7766 (mt-10) REVERT: B 196 ARG cc_start: 0.7848 (mtp-110) cc_final: 0.7556 (mtp-110) REVERT: B 201 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 219 LYS cc_start: 0.7734 (pttt) cc_final: 0.7209 (pttt) REVERT: B 244 PHE cc_start: 0.8145 (m-80) cc_final: 0.7723 (m-80) REVERT: B 263 TYR cc_start: 0.8212 (t80) cc_final: 0.7815 (t80) REVERT: B 295 PHE cc_start: 0.6997 (m-10) cc_final: 0.6787 (m-10) REVERT: B 306 ASN cc_start: 0.8443 (m110) cc_final: 0.8226 (m110) REVERT: B 310 TYR cc_start: 0.7123 (p90) cc_final: 0.6823 (p90) REVERT: B 317 GLN cc_start: 0.8865 (mm110) cc_final: 0.8647 (mm-40) REVERT: C 20 LEU cc_start: 0.8752 (tp) cc_final: 0.8544 (tp) REVERT: C 32 TYR cc_start: 0.7308 (t80) cc_final: 0.6941 (t80) REVERT: C 46 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7305 (mtmt) REVERT: C 85 PHE cc_start: 0.6585 (p90) cc_final: 0.6358 (p90) REVERT: C 89 LYS cc_start: 0.8313 (tttt) cc_final: 0.8046 (tttt) REVERT: C 114 MET cc_start: 0.7641 (mmm) cc_final: 0.7350 (mtm) REVERT: C 149 ASP cc_start: 0.9005 (m-30) cc_final: 0.8739 (m-30) REVERT: C 160 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8759 (ttmt) REVERT: C 207 ASN cc_start: 0.8393 (t0) cc_final: 0.8019 (p0) REVERT: C 221 ASP cc_start: 0.7095 (t0) cc_final: 0.6747 (t0) REVERT: C 282 ASP cc_start: 0.6689 (m-30) cc_final: 0.6429 (m-30) REVERT: C 303 PHE cc_start: 0.7209 (m-80) cc_final: 0.6915 (m-80) REVERT: C 319 ASP cc_start: 0.7710 (p0) cc_final: 0.7313 (p0) REVERT: C 321 ASP cc_start: 0.6102 (p0) cc_final: 0.5756 (p0) REVERT: D 205 MET cc_start: 0.4074 (mtm) cc_final: 0.3452 (mtm) REVERT: E 346 MET cc_start: 0.1736 (ptt) cc_final: 0.1516 (ptt) REVERT: E 348 MET cc_start: -0.0782 (pmm) cc_final: -0.1512 (pmm) REVERT: F 166 VAL cc_start: 0.7438 (m) cc_final: 0.7149 (p) REVERT: F 266 ILE cc_start: 0.7861 (mt) cc_final: 0.7461 (mt) REVERT: F 305 ILE cc_start: 0.7311 (mt) cc_final: 0.7094 (mt) REVERT: F 306 VAL cc_start: 0.8865 (t) cc_final: 0.8515 (p) REVERT: F 336 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.8280 (mtt-85) REVERT: F 346 GLN cc_start: 0.6941 (tp-100) cc_final: 0.6554 (tp-100) REVERT: F 397 ASN cc_start: 0.4396 (p0) cc_final: 0.4063 (p0) REVERT: F 548 ASP cc_start: 0.6154 (m-30) cc_final: 0.5847 (t0) REVERT: F 565 ILE cc_start: 0.4028 (mp) cc_final: 0.3038 (mp) REVERT: F 592 TYR cc_start: 0.6873 (t80) cc_final: 0.6438 (t80) outliers start: 1 outliers final: 0 residues processed: 462 average time/residue: 0.7406 time to fit residues: 505.1569 Evaluate side-chains 441 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18960 Z= 0.317 Angle : 0.656 8.569 25744 Z= 0.372 Chirality : 0.046 0.179 2697 Planarity : 0.005 0.065 3458 Dihedral : 5.722 38.137 2678 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.10 % Allowed : 0.42 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2401 helix: 0.37 (0.32), residues: 256 sheet: -0.58 (0.15), residues: 1091 loop : -1.66 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 516 HIS 0.013 0.002 HIS F 368 PHE 0.034 0.002 PHE A 118 TYR 0.025 0.002 TYR E 216 ARG 0.013 0.001 ARG B 270 ********************** 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 459 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 2.314 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: symmetry clash REVERT: A 13 LEU cc_start: 0.8337 (tp) cc_final: 0.8100 (tp) REVERT: A 38 MET cc_start: 0.8374 (mmt) cc_final: 0.8077 (mmm) REVERT: A 65 PHE cc_start: 0.7367 (m-10) cc_final: 0.7120 (m-10) REVERT: A 85 PHE cc_start: 0.6536 (p90) cc_final: 0.5836 (p90) REVERT: A 101 ASN cc_start: 0.7687 (t0) cc_final: 0.7487 (t0) REVERT: A 113 ASP cc_start: 0.8061 (t0) cc_final: 0.7514 (t0) REVERT: A 161 ASN cc_start: 0.8694 (t0) cc_final: 0.8376 (t0) REVERT: A 258 LEU cc_start: 0.7260 (mm) cc_final: 0.6989 (mm) REVERT: A 267 PHE cc_start: 0.8729 (p90) cc_final: 0.8372 (p90) REVERT: A 303 PHE cc_start: 0.8644 (m-80) cc_final: 0.8123 (m-80) REVERT: B 4 TYR cc_start: 0.8109 (t80) cc_final: 0.7661 (t80) REVERT: B 6 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8123 (ttpt) REVERT: B 40 TYR cc_start: 0.8186 (p90) cc_final: 0.7591 (p90) REVERT: B 65 PHE cc_start: 0.8207 (m-10) cc_final: 0.7758 (m-10) REVERT: B 76 GLN cc_start: 0.8558 (mp10) cc_final: 0.8258 (mp10) REVERT: B 80 LYS cc_start: 0.8920 (ptpp) cc_final: 0.8261 (ptpp) REVERT: B 81 THR cc_start: 0.8391 (p) cc_final: 0.8171 (p) REVERT: B 109 LEU cc_start: 0.8353 (mt) cc_final: 0.8087 (mt) REVERT: B 114 MET cc_start: 0.8025 (tpt) cc_final: 0.7815 (tpt) REVERT: B 121 ASP cc_start: 0.7511 (m-30) cc_final: 0.7294 (m-30) REVERT: B 124 TYR cc_start: 0.7659 (m-80) cc_final: 0.7251 (m-80) REVERT: B 183 GLU cc_start: 0.8411 (tt0) cc_final: 0.7738 (mt-10) REVERT: B 219 LYS cc_start: 0.7763 (pttt) cc_final: 0.7190 (pttt) REVERT: B 263 TYR cc_start: 0.8247 (t80) cc_final: 0.7748 (t80) REVERT: B 269 LEU cc_start: 0.8317 (tp) cc_final: 0.8113 (tp) REVERT: B 295 PHE cc_start: 0.7039 (m-10) cc_final: 0.6819 (m-10) REVERT: B 306 ASN cc_start: 0.8372 (m110) cc_final: 0.8131 (m110) REVERT: B 310 TYR cc_start: 0.7187 (p90) cc_final: 0.6885 (p90) REVERT: B 317 GLN cc_start: 0.8817 (mm110) cc_final: 0.8605 (mm-40) REVERT: C 7 ASP cc_start: 0.7961 (m-30) cc_final: 0.7736 (m-30) REVERT: C 32 TYR cc_start: 0.7216 (t80) cc_final: 0.6744 (t80) REVERT: C 85 PHE cc_start: 0.6572 (p90) cc_final: 0.6308 (p90) REVERT: C 89 LYS cc_start: 0.8306 (tttt) cc_final: 0.8067 (tttt) REVERT: C 114 MET cc_start: 0.7681 (mmm) cc_final: 0.7367 (mtm) REVERT: C 149 ASP cc_start: 0.8992 (m-30) cc_final: 0.8677 (m-30) REVERT: C 160 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8750 (ttmt) REVERT: C 207 ASN cc_start: 0.8393 (t0) cc_final: 0.8041 (p0) REVERT: C 221 ASP cc_start: 0.6952 (t0) cc_final: 0.6593 (t0) REVERT: C 224 ASN cc_start: 0.7083 (m110) cc_final: 0.6862 (m110) REVERT: C 282 ASP cc_start: 0.6635 (m-30) cc_final: 0.6396 (m-30) REVERT: C 303 PHE cc_start: 0.7385 (m-80) cc_final: 0.6854 (m-80) REVERT: C 319 ASP cc_start: 0.7870 (p0) cc_final: 0.7467 (p0) REVERT: C 321 ASP cc_start: 0.5928 (p0) cc_final: 0.5565 (p0) REVERT: D 205 MET cc_start: 0.3906 (mtm) cc_final: 0.3240 (mtm) REVERT: E 142 ARG cc_start: 0.3930 (mtp85) cc_final: 0.3166 (mtp85) REVERT: E 346 MET cc_start: 0.1762 (ptt) cc_final: 0.1531 (ptt) REVERT: E 348 MET cc_start: -0.0820 (pmm) cc_final: -0.1515 (pmm) REVERT: F 166 VAL cc_start: 0.7686 (m) cc_final: 0.7414 (p) REVERT: F 266 ILE cc_start: 0.7903 (mt) cc_final: 0.7497 (mt) REVERT: F 305 ILE cc_start: 0.7240 (mt) cc_final: 0.6749 (mt) REVERT: F 306 VAL cc_start: 0.8927 (t) cc_final: 0.8620 (p) REVERT: F 336 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8290 (mtt-85) REVERT: F 346 GLN cc_start: 0.6937 (tp-100) cc_final: 0.6573 (tp-100) REVERT: F 397 ASN cc_start: 0.4404 (p0) cc_final: 0.4041 (p0) REVERT: F 548 ASP cc_start: 0.6134 (m-30) cc_final: 0.5834 (t0) REVERT: F 565 ILE cc_start: 0.4094 (mp) cc_final: 0.3220 (mp) REVERT: F 592 TYR cc_start: 0.6850 (t80) cc_final: 0.6366 (t80) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.7405 time to fit residues: 499.8296 Evaluate side-chains 439 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 175 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** 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 = 0.4799 r_free = 0.4799 target = 0.222093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.172764 restraints weight = 182285.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.184010 restraints weight = 93370.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.191191 restraints weight = 52318.900| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4435 r_free = 0.4435 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4434 r_free = 0.4434 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 90 | |-----------------------------------------------------------------------------| r_final: 0.4434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18960 Z= 0.154 Angle : 0.552 6.556 25744 Z= 0.307 Chirality : 0.045 0.194 2697 Planarity : 0.004 0.058 3458 Dihedral : 5.185 33.285 2678 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.16 % Allowed : 0.21 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2401 helix: 1.57 (0.34), residues: 232 sheet: -0.40 (0.15), residues: 1099 loop : -1.24 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 516 HIS 0.007 0.001 HIS F 477 PHE 0.039 0.002 PHE A 118 TYR 0.016 0.001 TYR B 32 ARG 0.008 0.001 ARG D 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9595.78 seconds wall clock time: 169 minutes 35.68 seconds (10175.68 seconds total)