Starting phenix.real_space_refine on Wed Nov 22 00:35:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/11_2023/7nsu_12577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/11_2023/7nsu_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_12577/11_2023/7nsu_12577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/11_2023/7nsu_12577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/11_2023/7nsu_12577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/11_2023/7nsu_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 18.45, per 1000 atoms: 0.51 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: 32.14 Conformation dependent library (CDL) restraints added in 5.3 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: 3.87 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: 15.95 Time building geometry restraints manager: 32.77 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: 13361 17.98 - 35.96: 995 35.96 - 53.94: 222 53.94 - 71.93: 61 71.93 - 89.91: 14 Dihedral angle restraints: 14653 sinusoidal: 6459 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 14650 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: 1.830 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: 0.570 Extract box with map and model: 6.560 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 122.660 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.670 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.821 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 outliers start: 68 outliers final: 35 residues processed: 547 average time/residue: 0.7632 time to fit residues: 608.1219 Evaluate side-chains 472 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 437 time to evaluate : 2.623 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 7 residues processed: 35 average time/residue: 0.6472 time to fit residues: 38.6182 ------------------------------------------------------------------------------- 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: 9.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 50.0000 chunk 140 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 18960 Z= 0.401 Angle : 0.765 10.107 25744 Z= 0.431 Chirality : 0.048 0.225 2697 Planarity : 0.007 0.104 3458 Dihedral : 5.516 26.234 2678 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 0.52 % Allowed : 3.19 % Favored : 96.28 % 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: -1.16 (0.16), residues: 2401 helix: -0.43 (0.29), residues: 256 sheet: -0.38 (0.15), residues: 1111 loop : -1.17 (0.19), residues: 1034 *********************** 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: 8 poor density : 462 time to evaluate : 2.593 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 outliers start: 8 outliers final: 5 residues processed: 468 average time/residue: 0.7468 time to fit residues: 513.4238 Evaluate side-chains 431 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 426 time to evaluate : 2.549 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6907 time to fit residues: 8.6438 ------------------------------------------------------------------------------- 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: 10.0000 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 148 optimal weight: 50.0000 chunk 60 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 ASN F 502 GLN F 521 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5299 moved from start: 0.3356 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= 0.222 Angle : 0.581 8.574 25744 Z= 0.325 Chirality : 0.044 0.149 2697 Planarity : 0.005 0.052 3458 Dihedral : 5.096 30.656 2678 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.10 % Allowed : 2.09 % Favored : 97.80 % 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: -0.75 (0.17), residues: 2401 helix: 0.76 (0.32), residues: 252 sheet: -0.22 (0.15), residues: 1107 loop : -1.02 (0.19), residues: 1042 *********************** 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 447 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 2.857 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 outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.7356 time to fit residues: 483.6614 Evaluate side-chains 415 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.544 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3632 ------------------------------------------------------------------------------- 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: 5.9990 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** B 156 GLN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN D 409 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5500 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 18960 Z= 0.415 Angle : 0.740 9.681 25744 Z= 0.419 Chirality : 0.046 0.189 2697 Planarity : 0.006 0.084 3458 Dihedral : 5.608 29.049 2678 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 27.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.21 % Allowed : 2.67 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.17), residues: 2401 helix: 0.28 (0.30), residues: 255 sheet: -0.41 (0.15), residues: 1125 loop : -1.44 (0.19), residues: 1021 *********************** 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 468 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 466 time to evaluate : 2.840 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 outliers start: 2 outliers final: 1 residues processed: 468 average time/residue: 0.7484 time to fit residues: 520.1804 Evaluate side-chains 438 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 2.729 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4309 time to fit residues: 4.3488 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN E 87 GLN ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18960 Z= 0.301 Angle : 0.636 8.209 25744 Z= 0.359 Chirality : 0.045 0.188 2697 Planarity : 0.005 0.083 3458 Dihedral : 5.433 24.954 2678 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.26 % Allowed : 1.73 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.03 (0.17), residues: 2401 helix: 1.11 (0.33), residues: 234 sheet: -0.39 (0.15), residues: 1123 loop : -1.35 (0.19), residues: 1044 *********************** 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 473 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 2.599 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 outliers start: 3 outliers final: 1 residues processed: 472 average time/residue: 0.7654 time to fit residues: 534.4630 Evaluate side-chains 439 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4078 time to fit residues: 4.2049 ------------------------------------------------------------------------------- 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: 4.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 50.0000 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN ** B 306 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** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18960 Z= 0.276 Angle : 0.611 7.910 25744 Z= 0.344 Chirality : 0.044 0.159 2697 Planarity : 0.005 0.083 3458 Dihedral : 5.331 28.301 2678 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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: -1.07 (0.17), residues: 2401 helix: 0.80 (0.32), residues: 255 sheet: -0.39 (0.15), residues: 1123 loop : -1.38 (0.19), residues: 1023 *********************** 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 458 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 457 time to evaluate : 2.839 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 outliers start: 1 outliers final: 1 residues processed: 458 average time/residue: 0.7675 time to fit residues: 519.0817 Evaluate side-chains 430 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 429 time to evaluate : 2.352 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3706 time to fit residues: 3.9954 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 144 optimal weight: 40.0000 chunk 141 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 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 52 ASN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 224 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.5734 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= 0.446 Angle : 0.768 10.046 25744 Z= 0.435 Chirality : 0.047 0.287 2697 Planarity : 0.006 0.073 3458 Dihedral : 5.970 36.774 2678 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 34.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.16 % Allowed : 2.30 % Favored : 97.54 % 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: -1.58 (0.17), residues: 2401 helix: 0.06 (0.31), residues: 252 sheet: -0.63 (0.15), residues: 1094 loop : -1.70 (0.18), residues: 1055 *********************** 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 468 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 467 time to evaluate : 2.746 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.7650 time to fit residues: 528.7442 Evaluate side-chains 441 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.649 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2746 ------------------------------------------------------------------------------- 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: 0.9980 chunk 92 optimal weight: 0.0670 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 157 optimal weight: 10.0000 chunk 114 optimal weight: 50.0000 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18960 Z= 0.170 Angle : 0.577 6.542 25744 Z= 0.319 Chirality : 0.045 0.185 2697 Planarity : 0.005 0.119 3458 Dihedral : 5.291 28.914 2678 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.37 % 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: -0.95 (0.17), residues: 2401 helix: 1.49 (0.34), residues: 234 sheet: -0.39 (0.15), residues: 1105 loop : -1.31 (0.19), residues: 1062 *********************** 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 461 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 2.597 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 outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.7565 time to fit residues: 515.0067 Evaluate side-chains 429 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 2.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5071 ------------------------------------------------------------------------------- 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: 8.9990 chunk 221 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18960 Z= 0.289 Angle : 0.621 8.557 25744 Z= 0.349 Chirality : 0.044 0.160 2697 Planarity : 0.005 0.078 3458 Dihedral : 5.415 29.429 2678 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.37 % 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 (0.17), residues: 2401 helix: 0.82 (0.32), residues: 255 sheet: -0.51 (0.15), residues: 1104 loop : -1.49 (0.18), residues: 1042 *********************** 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 456 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 3.430 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.7676 time to fit residues: 514.8585 Evaluate side-chains 435 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7614 ------------------------------------------------------------------------------- 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: 1.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 HIS ** B 252 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** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5502 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18960 Z= 0.251 Angle : 0.607 7.855 25744 Z= 0.340 Chirality : 0.044 0.168 2697 Planarity : 0.005 0.082 3458 Dihedral : 5.422 28.052 2678 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.33), residues: 234 sheet: -0.52 (0.15), residues: 1092 loop : -1.48 (0.18), residues: 1075 ********************** 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 454 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 2.760 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 outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.7549 time to fit residues: 501.3263 Evaluate side-chains 433 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 2.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7158 ------------------------------------------------------------------------------- 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: 7.9990 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 0.0970 chunk 195 optimal weight: 6.9990 chunk 24 optimal weight: 0.0970 chunk 35 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4809 r_free = 0.4809 target = 0.222399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.168352 restraints weight = 181716.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.180823 restraints weight = 92212.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.188600 restraints weight = 51358.536| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4421 r_free = 0.4421 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.4421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18960 Z= 0.160 Angle : 0.543 5.817 25744 Z= 0.302 Chirality : 0.044 0.181 2697 Planarity : 0.004 0.058 3458 Dihedral : 5.099 26.979 2678 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.10 % Allowed : 0.26 % 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: -0.92 (0.17), residues: 2401 helix: 1.78 (0.34), residues: 235 sheet: -0.40 (0.16), residues: 1044 loop : -1.29 (0.18), residues: 1122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9942.57 seconds wall clock time: 177 minutes 33.48 seconds (10653.48 seconds total)