Starting phenix.real_space_refine on Thu Sep 26 17:56:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/09_2024/7ysr_34081.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/09_2024/7ysr_34081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/09_2024/7ysr_34081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/09_2024/7ysr_34081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/09_2024/7ysr_34081.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysr_34081/09_2024/7ysr_34081.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 98 5.16 5 C 8462 2.51 5 N 2298 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13456 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3314 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "C" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3314 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.28, per 1000 atoms: 0.84 Number of scatterers: 13456 At special positions: 0 Unit cell: (112.32, 109.08, 122.04, 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 98 16.00 P 12 15.00 O 2586 8.00 N 2298 7.00 C 8462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 54.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.767A pdb=" N VAL A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.967A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 128 removed outlier: 5.842A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.421A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.503A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.812A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.583A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 4.026A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 382 through 398 removed outlier: 4.117A pdb=" N GLU A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.817A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.883A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.106A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 129 removed outlier: 4.055A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 removed outlier: 3.853A pdb=" N SER B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.043A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.467A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.686A pdb=" N GLN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.928A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.548A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 382 through 398 removed outlier: 4.190A pdb=" N GLU B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 removed outlier: 4.415A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 71 through 80 removed outlier: 4.854A pdb=" N VAL C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 128 removed outlier: 5.711A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 162 removed outlier: 4.360A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.546A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.690A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.785A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 382 through 398 removed outlier: 3.912A pdb=" N GLU C 386 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.772A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.939A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 40 through 48 removed outlier: 4.029A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.803A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 110 through 129 removed outlier: 4.176A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 removed outlier: 3.752A pdb=" N SER D 147 " --> pdb=" O GLY D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 4.537A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.504A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 279 through 284 removed outlier: 4.031A pdb=" N ARG D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 382 through 400 removed outlier: 4.205A pdb=" N GLU D 386 " --> pdb=" O THR D 382 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 4.440A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 435 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.539A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N SER A 140 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL A 9 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 4.039A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.821A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASN A 356 " --> pdb=" O MET A 317 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.039A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 5 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 165 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.846A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 68 removed outlier: 8.662A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE C 171 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.979A pdb=" N LYS C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.501A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS C 376 " --> pdb=" O MET C 317 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N LYS C 352 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS C 315 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY C 354 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 317 " --> pdb=" O GLY C 354 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN C 356 " --> pdb=" O MET C 317 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR C 319 " --> pdb=" O ASN C 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 94 removed outlier: 8.013A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLU D 3 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER D 140 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TYR D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU D 137 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 648 hydrogen bonds defined for protein. 1857 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: 4.38 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4452 1.34 - 1.46: 3244 1.46 - 1.58: 5894 1.58 - 1.70: 22 1.70 - 1.82: 152 Bond restraints: 13764 Sorted by residual: bond pdb=" C ARG A 320 " pdb=" N GLY A 321 " ideal model delta sigma weight residual 1.334 1.322 0.012 1.12e-02 7.97e+03 1.20e+00 bond pdb=" CB LYS D 124 " pdb=" CG LYS D 124 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.64e-01 bond pdb=" C VAL D 62 " pdb=" O VAL D 62 " ideal model delta sigma weight residual 1.232 1.241 -0.008 8.90e-03 1.26e+04 8.62e-01 bond pdb=" CA ILE C 171 " pdb=" CB ILE C 171 " ideal model delta sigma weight residual 1.527 1.538 -0.012 1.31e-02 5.83e+03 7.94e-01 bond pdb=" C SER B 324 " pdb=" N MET B 325 " ideal model delta sigma weight residual 1.333 1.320 0.013 1.56e-02 4.11e+03 7.24e-01 ... (remaining 13759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 18252 1.61 - 3.22: 371 3.22 - 4.83: 45 4.83 - 6.44: 16 6.44 - 8.05: 10 Bond angle restraints: 18694 Sorted by residual: angle pdb=" CA MET B 325 " pdb=" C MET B 325 " pdb=" N LYS B 326 " ideal model delta sigma weight residual 118.59 123.67 -5.08 1.63e+00 3.76e-01 9.72e+00 angle pdb=" C ARG C 214 " pdb=" N ARG C 215 " pdb=" CA ARG C 215 " ideal model delta sigma weight residual 122.60 117.90 4.70 1.56e+00 4.11e-01 9.06e+00 angle pdb=" CA MET A 317 " pdb=" CB MET A 317 " pdb=" CG MET A 317 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.92e+00 angle pdb=" CB MET A 317 " pdb=" CG MET A 317 " pdb=" SD MET A 317 " ideal model delta sigma weight residual 112.70 120.75 -8.05 3.00e+00 1.11e-01 7.21e+00 angle pdb=" CB MET D 332 " pdb=" CG MET D 332 " pdb=" SD MET D 332 " ideal model delta sigma weight residual 112.70 120.58 -7.88 3.00e+00 1.11e-01 6.90e+00 ... (remaining 18689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 8019 35.37 - 70.74: 142 70.74 - 106.12: 11 106.12 - 141.49: 3 141.49 - 176.86: 1 Dihedral angle restraints: 8176 sinusoidal: 3280 harmonic: 4896 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -113.87 -176.86 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -157.88 -132.85 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -11.36 115.95 1 2.00e+01 2.50e-03 3.45e+01 ... (remaining 8173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1346 0.036 - 0.072: 474 0.072 - 0.109: 175 0.109 - 0.145: 43 0.145 - 0.181: 4 Chirality restraints: 2042 Sorted by residual: chirality pdb=" CB ILE D 318 " pdb=" CA ILE D 318 " pdb=" CG1 ILE D 318 " pdb=" CG2 ILE D 318 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB THR D 221 " pdb=" CA THR D 221 " pdb=" OG1 THR D 221 " pdb=" CG2 THR D 221 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB THR B 221 " pdb=" CA THR B 221 " pdb=" OG1 THR B 221 " pdb=" CG2 THR B 221 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 2039 not shown) Planarity restraints: 2426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 389 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C LYS B 389 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS B 389 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 390 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 89 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 123 " 0.130 9.50e-02 1.11e+02 5.83e-02 2.14e+00 pdb=" NE ARG A 123 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 123 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 123 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 123 " 0.006 2.00e-02 2.50e+03 ... (remaining 2423 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 359 2.69 - 3.25: 14507 3.25 - 3.80: 23270 3.80 - 4.35: 28990 4.35 - 4.90: 47830 Nonbonded interactions: 114956 Sorted by model distance: nonbonded pdb=" OH TYR B 185 " pdb=" O MET B 398 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR D 185 " pdb=" O MET D 398 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR C 185 " pdb=" O MET C 398 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR A 185 " pdb=" O MET A 398 " model vdw 2.166 3.040 nonbonded pdb=" NH1 ARG C 215 " pdb=" OD1 ASN C 216 " model vdw 2.173 3.120 ... (remaining 114951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 23.950 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.120 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 0.028 13764 Z= 0.189 Angle : 0.590 8.053 18694 Z= 0.308 Chirality : 0.043 0.181 2042 Planarity : 0.004 0.058 2426 Dihedral : 14.906 176.861 5040 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.51 (0.21), residues: 1684 helix: 1.05 (0.19), residues: 746 sheet: 0.30 (0.32), residues: 280 loop : -0.36 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 21 HIS 0.005 0.001 HIS A 197 PHE 0.013 0.001 PHE B 377 TYR 0.021 0.001 TYR C 224 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.8338 (ptt) cc_final: 0.7980 (ptt) REVERT: D 124 LYS cc_start: 0.9584 (tmtt) cc_final: 0.9361 (tptp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2758 time to fit residues: 52.6199 Evaluate side-chains 95 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 0.0470 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 206 ASN B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 283 HIS ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13764 Z= 0.300 Angle : 0.604 7.680 18694 Z= 0.312 Chirality : 0.044 0.165 2042 Planarity : 0.004 0.064 2426 Dihedral : 8.803 175.931 1902 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.35 % Allowed : 7.00 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.69 (0.20), residues: 1684 helix: 1.24 (0.18), residues: 770 sheet: 0.18 (0.31), residues: 282 loop : -0.28 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 21 HIS 0.008 0.001 HIS C 266 PHE 0.013 0.001 PHE A 138 TYR 0.014 0.002 TYR A 282 ARG 0.005 0.001 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8071 (mpp) cc_final: 0.7847 (mpp) REVERT: A 377 MET cc_start: 0.8315 (ppp) cc_final: 0.7947 (ppp) REVERT: B 124 LYS cc_start: 0.9450 (tmtt) cc_final: 0.9197 (tptp) REVERT: D 75 MET cc_start: 0.7934 (mtp) cc_final: 0.7692 (mtp) REVERT: D 124 LYS cc_start: 0.9539 (tmtt) cc_final: 0.9316 (tptp) REVERT: D 299 LYS cc_start: 0.8625 (ptmm) cc_final: 0.8369 (tmmt) REVERT: D 301 MET cc_start: 0.8623 (mmm) cc_final: 0.8295 (mmp) REVERT: D 302 MET cc_start: 0.8419 (mtm) cc_final: 0.8111 (mtm) outliers start: 5 outliers final: 2 residues processed: 125 average time/residue: 0.2709 time to fit residues: 49.4433 Evaluate side-chains 91 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 151 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 193 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13764 Z= 0.236 Angle : 0.580 7.641 18694 Z= 0.297 Chirality : 0.044 0.183 2042 Planarity : 0.004 0.062 2426 Dihedral : 8.768 175.271 1902 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.14 % Allowed : 4.99 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1684 helix: 1.25 (0.18), residues: 768 sheet: 0.18 (0.31), residues: 282 loop : -0.30 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.007 0.001 HIS C 192 PHE 0.020 0.001 PHE B 214 TYR 0.021 0.001 TYR A 224 ARG 0.008 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8348 (t80) cc_final: 0.8033 (t80) REVERT: A 313 MET cc_start: 0.8062 (mpp) cc_final: 0.7767 (mpp) REVERT: B 124 LYS cc_start: 0.9511 (tmtt) cc_final: 0.9183 (tptp) REVERT: B 301 MET cc_start: 0.8402 (mmp) cc_final: 0.8151 (mmp) REVERT: B 325 MET cc_start: 0.8395 (ptt) cc_final: 0.7968 (ptt) REVERT: C 215 ARG cc_start: 0.9061 (pmt-80) cc_final: 0.8463 (pmt-80) REVERT: D 75 MET cc_start: 0.7927 (mtp) cc_final: 0.7651 (mtp) REVERT: D 124 LYS cc_start: 0.9501 (tmtt) cc_final: 0.9290 (tptp) REVERT: D 299 LYS cc_start: 0.8959 (ptmm) cc_final: 0.8551 (tmmt) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.3008 time to fit residues: 55.6468 Evaluate side-chains 96 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 256 GLN B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13764 Z= 0.287 Angle : 0.606 7.832 18694 Z= 0.312 Chirality : 0.044 0.178 2042 Planarity : 0.004 0.034 2426 Dihedral : 8.823 173.269 1902 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.54 (0.20), residues: 1684 helix: 1.08 (0.18), residues: 784 sheet: 0.28 (0.31), residues: 270 loop : -0.41 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 21 HIS 0.012 0.001 HIS C 266 PHE 0.014 0.001 PHE D 92 TYR 0.016 0.001 TYR A 224 ARG 0.008 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8397 (t80) cc_final: 0.7777 (t80) REVERT: A 313 MET cc_start: 0.8060 (mpp) cc_final: 0.7855 (mpp) REVERT: B 124 LYS cc_start: 0.9431 (tmtt) cc_final: 0.9149 (tptp) REVERT: B 127 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8603 (mm-30) REVERT: B 301 MET cc_start: 0.8493 (mmp) cc_final: 0.8277 (mmp) REVERT: C 154 MET cc_start: 0.8288 (ttt) cc_final: 0.8038 (ttt) REVERT: D 75 MET cc_start: 0.7823 (mtp) cc_final: 0.7539 (mtp) REVERT: D 124 LYS cc_start: 0.9497 (tmtt) cc_final: 0.9287 (tptp) REVERT: D 295 MET cc_start: 0.8200 (tpt) cc_final: 0.7912 (tpp) REVERT: D 299 LYS cc_start: 0.8944 (ptmm) cc_final: 0.8667 (ptmm) REVERT: D 302 MET cc_start: 0.8489 (mtm) cc_final: 0.8148 (mtm) REVERT: D 325 MET cc_start: 0.8795 (pmm) cc_final: 0.8189 (ptp) outliers start: 2 outliers final: 0 residues processed: 121 average time/residue: 0.2796 time to fit residues: 48.8272 Evaluate side-chains 90 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 256 GLN C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13764 Z= 0.213 Angle : 0.588 7.615 18694 Z= 0.299 Chirality : 0.044 0.175 2042 Planarity : 0.004 0.029 2426 Dihedral : 8.742 171.551 1902 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1684 helix: 1.19 (0.18), residues: 778 sheet: 0.29 (0.31), residues: 270 loop : -0.45 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.009 0.001 HIS C 266 PHE 0.014 0.001 PHE B 388 TYR 0.011 0.001 TYR A 224 ARG 0.007 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8356 (t80) cc_final: 0.7700 (t80) REVERT: A 313 MET cc_start: 0.8099 (mpp) cc_final: 0.7894 (mpp) REVERT: B 124 LYS cc_start: 0.9386 (tmtt) cc_final: 0.9119 (tptp) REVERT: B 301 MET cc_start: 0.8466 (mmp) cc_final: 0.8251 (mmp) REVERT: C 377 MET cc_start: 0.8386 (ppp) cc_final: 0.8186 (ppp) REVERT: D 75 MET cc_start: 0.7779 (mtp) cc_final: 0.7492 (mtp) REVERT: D 124 LYS cc_start: 0.9471 (tmtt) cc_final: 0.9265 (tptp) REVERT: D 295 MET cc_start: 0.8206 (tpt) cc_final: 0.7953 (tpp) REVERT: D 299 LYS cc_start: 0.8920 (ptmm) cc_final: 0.8434 (tmmt) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.2857 time to fit residues: 50.4530 Evaluate side-chains 87 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.0270 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 436 GLN C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13764 Z= 0.226 Angle : 0.589 8.052 18694 Z= 0.300 Chirality : 0.044 0.171 2042 Planarity : 0.004 0.033 2426 Dihedral : 8.706 169.318 1902 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1684 helix: 1.16 (0.18), residues: 782 sheet: 0.33 (0.31), residues: 270 loop : -0.45 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.009 0.001 HIS C 266 PHE 0.011 0.001 PHE C 149 TYR 0.010 0.001 TYR A 224 ARG 0.010 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8362 (t80) cc_final: 0.7727 (t80) REVERT: A 377 MET cc_start: 0.8335 (ppp) cc_final: 0.7915 (ppp) REVERT: B 124 LYS cc_start: 0.9411 (tmtt) cc_final: 0.9144 (tptp) REVERT: B 301 MET cc_start: 0.8491 (mmp) cc_final: 0.8285 (mmp) REVERT: C 377 MET cc_start: 0.8353 (ppp) cc_final: 0.7574 (ppp) REVERT: D 75 MET cc_start: 0.7784 (mtp) cc_final: 0.7498 (mtp) REVERT: D 124 LYS cc_start: 0.9469 (tmtt) cc_final: 0.9264 (tptp) REVERT: D 295 MET cc_start: 0.8285 (tpt) cc_final: 0.8032 (tpp) REVERT: D 299 LYS cc_start: 0.8908 (ptmm) cc_final: 0.8607 (ptmm) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.3039 time to fit residues: 53.9042 Evaluate side-chains 91 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 0.0670 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13764 Z= 0.174 Angle : 0.582 7.390 18694 Z= 0.296 Chirality : 0.044 0.175 2042 Planarity : 0.003 0.034 2426 Dihedral : 8.612 166.876 1902 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.66 (0.20), residues: 1684 helix: 1.21 (0.18), residues: 782 sheet: 0.34 (0.31), residues: 270 loop : -0.40 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.007 0.001 HIS C 266 PHE 0.012 0.001 PHE C 138 TYR 0.010 0.001 TYR C 224 ARG 0.007 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8320 (t80) cc_final: 0.7652 (t80) REVERT: A 377 MET cc_start: 0.8333 (ppp) cc_final: 0.7901 (ppp) REVERT: B 124 LYS cc_start: 0.9381 (tmtt) cc_final: 0.9142 (tptp) REVERT: C 154 MET cc_start: 0.8165 (ttt) cc_final: 0.7851 (ttt) REVERT: D 75 MET cc_start: 0.7760 (mtp) cc_final: 0.7474 (mtp) REVERT: D 295 MET cc_start: 0.8258 (tpt) cc_final: 0.7893 (tpp) REVERT: D 325 MET cc_start: 0.8611 (pmm) cc_final: 0.7893 (ptp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3232 time to fit residues: 59.0906 Evaluate side-chains 90 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13764 Z= 0.190 Angle : 0.596 8.662 18694 Z= 0.301 Chirality : 0.044 0.162 2042 Planarity : 0.004 0.035 2426 Dihedral : 8.570 164.228 1902 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.61 (0.20), residues: 1684 helix: 1.23 (0.18), residues: 780 sheet: 0.24 (0.31), residues: 270 loop : -0.46 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.007 0.001 HIS C 266 PHE 0.024 0.001 PHE C 135 TYR 0.028 0.001 TYR A 224 ARG 0.007 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8348 (t80) cc_final: 0.7699 (t80) REVERT: A 377 MET cc_start: 0.8390 (ppp) cc_final: 0.7879 (ppp) REVERT: B 124 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9137 (tptp) REVERT: C 154 MET cc_start: 0.8203 (ttt) cc_final: 0.7976 (ttt) REVERT: C 377 MET cc_start: 0.8419 (ppp) cc_final: 0.8004 (ppp) REVERT: D 75 MET cc_start: 0.7732 (mtp) cc_final: 0.7439 (mtp) REVERT: D 124 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9166 (tptp) REVERT: D 302 MET cc_start: 0.8445 (mtm) cc_final: 0.8230 (mtm) REVERT: D 325 MET cc_start: 0.8581 (pmm) cc_final: 0.7930 (ptp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2826 time to fit residues: 50.7029 Evaluate side-chains 91 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 107 HIS D 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13764 Z= 0.215 Angle : 0.608 8.671 18694 Z= 0.306 Chirality : 0.044 0.196 2042 Planarity : 0.004 0.040 2426 Dihedral : 8.559 161.237 1902 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.07 % Allowed : 0.62 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1684 helix: 1.22 (0.18), residues: 782 sheet: 0.18 (0.31), residues: 270 loop : -0.46 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 21 HIS 0.006 0.001 HIS C 266 PHE 0.017 0.001 PHE C 135 TYR 0.025 0.001 TYR C 282 ARG 0.008 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8330 (t80) cc_final: 0.7659 (t80) REVERT: B 124 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9155 (tptp) REVERT: B 149 MET cc_start: 0.8844 (mmp) cc_final: 0.8603 (mmp) REVERT: C 154 MET cc_start: 0.8239 (ttt) cc_final: 0.8022 (ttt) REVERT: C 377 MET cc_start: 0.8444 (ppp) cc_final: 0.8009 (ppp) REVERT: D 75 MET cc_start: 0.7758 (mtp) cc_final: 0.7476 (mtp) REVERT: D 124 LYS cc_start: 0.9418 (tmtt) cc_final: 0.9205 (tptp) REVERT: D 295 MET cc_start: 0.8281 (tpt) cc_final: 0.7861 (tpp) REVERT: D 302 MET cc_start: 0.8450 (mtm) cc_final: 0.8161 (mtm) REVERT: D 325 MET cc_start: 0.8618 (pmm) cc_final: 0.7935 (ptp) REVERT: D 336 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7518 (tp-100) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.2819 time to fit residues: 49.1722 Evaluate side-chains 90 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 0.0000 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 6 HIS D 282 GLN D 331 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13764 Z= 0.149 Angle : 0.597 9.459 18694 Z= 0.298 Chirality : 0.044 0.192 2042 Planarity : 0.003 0.029 2426 Dihedral : 8.421 156.535 1902 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.72 (0.20), residues: 1684 helix: 1.38 (0.18), residues: 770 sheet: 0.18 (0.30), residues: 288 loop : -0.42 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 346 HIS 0.006 0.001 HIS C 266 PHE 0.012 0.001 PHE C 135 TYR 0.019 0.001 TYR A 224 ARG 0.007 0.000 ARG C 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8155 (t80) cc_final: 0.7567 (t80) REVERT: B 149 MET cc_start: 0.8682 (mmp) cc_final: 0.8465 (mmp) REVERT: C 377 MET cc_start: 0.8672 (ppp) cc_final: 0.8415 (ppp) REVERT: D 75 MET cc_start: 0.7698 (mtp) cc_final: 0.7432 (mtp) REVERT: D 302 MET cc_start: 0.8449 (mtm) cc_final: 0.8149 (mtm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2901 time to fit residues: 53.6341 Evaluate side-chains 89 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.045761 restraints weight = 74724.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.047104 restraints weight = 43748.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.048055 restraints weight = 29868.493| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13764 Z= 0.160 Angle : 0.589 8.398 18694 Z= 0.295 Chirality : 0.044 0.185 2042 Planarity : 0.003 0.039 2426 Dihedral : 8.387 154.178 1902 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.70 (0.20), residues: 1684 helix: 1.36 (0.18), residues: 772 sheet: 0.13 (0.30), residues: 292 loop : -0.40 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.006 0.001 HIS C 266 PHE 0.015 0.001 PHE A 149 TYR 0.020 0.001 TYR A 224 ARG 0.005 0.000 ARG C 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.17 seconds wall clock time: 47 minutes 44.50 seconds (2864.50 seconds total)