Starting phenix.real_space_refine on Thu Jul 31 18:20:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ysr_34081/07_2025/7ysr_34081.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ysr_34081/07_2025/7ysr_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/cci-nas-00/data/ceres_data/7ysr_34081/07_2025/7ysr_34081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ysr_34081/07_2025/7ysr_34081.map" model { file = "/net/cci-nas-00/data/ceres_data/7ysr_34081/07_2025/7ysr_34081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ysr_34081/07_2025/7ysr_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 11.17, per 1000 atoms: 0.83 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 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: 1.36 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: 4.05 Time building geometry restraints manager: 3.76 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: 0.03 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: 13.880 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: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.320 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- 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= 0.142 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 Details of bonding type rmsd hydrogen bonds : bond 0.14725 ( 648) hydrogen bonds : angle 6.13991 ( 1857) covalent geometry : bond 0.00293 (13764) covalent geometry : angle 0.58959 (18694) *********************** 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 to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.624 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: 0.2692 time to fit residues: 51.7857 Evaluate side-chains 95 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044084 restraints weight = 77970.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045343 restraints weight = 46495.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.046229 restraints weight = 32078.671| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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= 0.218 Angle : 0.604 7.680 18694 Z= 0.312 Chirality : 0.044 0.165 2042 Planarity : 0.004 0.064 2426 Dihedral : 8.803 175.930 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 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 648) hydrogen bonds : angle 4.94608 ( 1857) covalent geometry : bond 0.00460 (13764) covalent geometry : angle 0.60381 (18694) *********************** 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 to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8119 (mpp) cc_final: 0.7805 (mpp) REVERT: A 377 MET cc_start: 0.8335 (ppp) cc_final: 0.7954 (ppp) REVERT: B 124 LYS cc_start: 0.9436 (tmtt) cc_final: 0.9191 (tptp) REVERT: D 75 MET cc_start: 0.8019 (mtp) cc_final: 0.7793 (mtp) REVERT: D 124 LYS cc_start: 0.9521 (tmtt) cc_final: 0.9301 (tptp) REVERT: D 299 LYS cc_start: 0.8620 (ptmm) cc_final: 0.8359 (tmmt) REVERT: D 301 MET cc_start: 0.8623 (mmm) cc_final: 0.8316 (mmp) REVERT: D 302 MET cc_start: 0.8662 (mtm) cc_final: 0.8275 (mtm) REVERT: D 413 MET cc_start: 0.9064 (mmm) cc_final: 0.8839 (mmp) outliers start: 5 outliers final: 2 residues processed: 125 average time/residue: 0.2805 time to fit residues: 51.3059 Evaluate side-chains 91 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** B 433 GLN B 436 GLN C 128 GLN C 283 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.051682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.044660 restraints weight = 77460.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045929 restraints weight = 46525.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046844 restraints weight = 32068.225| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1285 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= 0.168 Angle : 0.577 7.622 18694 Z= 0.295 Chirality : 0.044 0.184 2042 Planarity : 0.004 0.062 2426 Dihedral : 8.765 175.350 1902 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.22 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: 0.69 (0.20), residues: 1684 helix: 1.26 (0.18), residues: 768 sheet: 0.18 (0.31), residues: 282 loop : -0.29 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 21 HIS 0.007 0.001 HIS C 192 PHE 0.020 0.001 PHE B 214 TYR 0.022 0.001 TYR A 224 ARG 0.009 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 648) hydrogen bonds : angle 4.79902 ( 1857) covalent geometry : bond 0.00358 (13764) covalent geometry : angle 0.57748 (18694) *********************** 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 131 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8336 (t80) cc_final: 0.8013 (t80) REVERT: A 313 MET cc_start: 0.8102 (mpp) cc_final: 0.7733 (mpp) REVERT: B 124 LYS cc_start: 0.9499 (tmtt) cc_final: 0.9165 (tptp) REVERT: B 301 MET cc_start: 0.8394 (mmp) cc_final: 0.8108 (mmp) REVERT: B 325 MET cc_start: 0.8490 (ptt) cc_final: 0.8030 (ptt) REVERT: D 75 MET cc_start: 0.7977 (mtp) cc_final: 0.7735 (mtp) REVERT: D 124 LYS cc_start: 0.9482 (tmtt) cc_final: 0.9271 (tptp) REVERT: D 295 MET cc_start: 0.7967 (tpp) cc_final: 0.7764 (tpp) REVERT: D 299 LYS cc_start: 0.8988 (ptmm) cc_final: 0.8540 (tmmt) outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.3002 time to fit residues: 55.7381 Evaluate side-chains 96 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 256 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.051792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044598 restraints weight = 76274.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045969 restraints weight = 44235.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046938 restraints weight = 29734.863| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13764 Z= 0.135 Angle : 0.564 7.428 18694 Z= 0.288 Chirality : 0.043 0.174 2042 Planarity : 0.003 0.029 2426 Dihedral : 8.698 173.755 1902 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.14 % Allowed : 3.40 % Favored : 96.46 % 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: 1.31 (0.18), residues: 768 sheet: 0.23 (0.31), residues: 284 loop : -0.33 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.012 0.001 HIS C 266 PHE 0.014 0.001 PHE D 92 TYR 0.013 0.001 TYR A 224 ARG 0.008 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 648) hydrogen bonds : angle 4.68998 ( 1857) covalent geometry : bond 0.00289 (13764) covalent geometry : angle 0.56358 (18694) *********************** 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 127 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.9182 (pptt) cc_final: 0.8979 (pptt) REVERT: A 172 TYR cc_start: 0.8355 (t80) cc_final: 0.7726 (t80) REVERT: A 313 MET cc_start: 0.8080 (mpp) cc_final: 0.7774 (mpp) REVERT: B 124 LYS cc_start: 0.9413 (tmtt) cc_final: 0.9128 (tptp) REVERT: B 301 MET cc_start: 0.8438 (mmp) cc_final: 0.8187 (mmp) REVERT: B 329 ASP cc_start: 0.9468 (m-30) cc_final: 0.9265 (m-30) REVERT: C 154 MET cc_start: 0.8226 (ttt) cc_final: 0.7959 (ttt) REVERT: C 377 MET cc_start: 0.8461 (ppp) cc_final: 0.8227 (ppp) REVERT: D 75 MET cc_start: 0.7870 (mtp) cc_final: 0.7617 (mtp) REVERT: D 124 LYS cc_start: 0.9466 (tmtt) cc_final: 0.9249 (tptp) REVERT: D 299 LYS cc_start: 0.8943 (ptmm) cc_final: 0.8454 (tmmt) REVERT: D 302 MET cc_start: 0.8761 (mtm) cc_final: 0.8295 (mtm) REVERT: D 325 MET cc_start: 0.8846 (pmm) cc_final: 0.8128 (ptp) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.2809 time to fit residues: 51.7861 Evaluate side-chains 96 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 165 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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** B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.051941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.044857 restraints weight = 76766.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046208 restraints weight = 44984.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.047156 restraints weight = 30332.277| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13764 Z= 0.141 Angle : 0.574 7.421 18694 Z= 0.292 Chirality : 0.044 0.173 2042 Planarity : 0.003 0.028 2426 Dihedral : 8.657 171.956 1902 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.73 (0.20), residues: 1684 helix: 1.32 (0.18), residues: 766 sheet: 0.24 (0.30), residues: 284 loop : -0.33 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.009 0.001 HIS C 266 PHE 0.012 0.001 PHE C 138 TYR 0.012 0.001 TYR A 224 ARG 0.007 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 648) hydrogen bonds : angle 4.68198 ( 1857) covalent geometry : bond 0.00302 (13764) covalent geometry : angle 0.57443 (18694) *********************** 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 125 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8335 (t80) cc_final: 0.7715 (t80) REVERT: A 313 MET cc_start: 0.8134 (mpp) cc_final: 0.7843 (mpp) REVERT: B 124 LYS cc_start: 0.9415 (tmtt) cc_final: 0.9121 (tptp) REVERT: B 301 MET cc_start: 0.8473 (mmp) cc_final: 0.8236 (mmp) REVERT: C 154 MET cc_start: 0.8406 (ttt) cc_final: 0.8177 (ttt) REVERT: C 377 MET cc_start: 0.8325 (ppp) cc_final: 0.7508 (ppp) REVERT: D 75 MET cc_start: 0.7831 (mtp) cc_final: 0.7574 (mtp) REVERT: D 124 LYS cc_start: 0.9464 (tmtt) cc_final: 0.9257 (tptp) REVERT: D 295 MET cc_start: 0.8398 (tpt) cc_final: 0.8108 (tpp) REVERT: D 299 LYS cc_start: 0.8933 (ptmm) cc_final: 0.8436 (tmmt) REVERT: D 325 MET cc_start: 0.8744 (pmm) cc_final: 0.8123 (ptp) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2711 time to fit residues: 49.3584 Evaluate side-chains 89 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 0.0170 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.044653 restraints weight = 77439.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.045953 restraints weight = 45370.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046896 restraints weight = 31081.025| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1604 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= 0.137 Angle : 0.569 8.548 18694 Z= 0.287 Chirality : 0.043 0.183 2042 Planarity : 0.003 0.028 2426 Dihedral : 8.621 169.870 1902 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.14 % Allowed : 2.36 % Favored : 97.50 % 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: 0.76 (0.20), residues: 1684 helix: 1.32 (0.18), residues: 780 sheet: 0.40 (0.31), residues: 270 loop : -0.38 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.007 0.001 HIS C 266 PHE 0.011 0.001 PHE B 388 TYR 0.010 0.001 TYR A 224 ARG 0.010 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 648) hydrogen bonds : angle 4.62649 ( 1857) covalent geometry : bond 0.00296 (13764) covalent geometry : angle 0.56912 (18694) *********************** 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 130 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8330 (t80) cc_final: 0.7705 (t80) REVERT: A 313 MET cc_start: 0.8123 (mpp) cc_final: 0.7833 (mpp) REVERT: A 377 MET cc_start: 0.8319 (ppp) cc_final: 0.7926 (ppp) REVERT: B 124 LYS cc_start: 0.9427 (tmtt) cc_final: 0.9146 (tptp) REVERT: B 301 MET cc_start: 0.8478 (mmp) cc_final: 0.8242 (mmp) REVERT: C 377 MET cc_start: 0.8367 (ppp) cc_final: 0.8012 (ppp) REVERT: D 75 MET cc_start: 0.7847 (mtp) cc_final: 0.7593 (mtp) REVERT: D 124 LYS cc_start: 0.9457 (tmtt) cc_final: 0.9246 (tptp) REVERT: D 299 LYS cc_start: 0.8908 (ptmm) cc_final: 0.8379 (ttpp) REVERT: D 302 MET cc_start: 0.8660 (mtm) cc_final: 0.8292 (mtm) REVERT: D 325 MET cc_start: 0.8593 (pmm) cc_final: 0.7966 (ptp) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.2615 time to fit residues: 50.0264 Evaluate side-chains 89 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 293 GLN ** 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** D 433 GLN D 436 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045143 restraints weight = 76788.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046438 restraints weight = 45335.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047377 restraints weight = 31102.371| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13764 Z= 0.161 Angle : 0.603 8.035 18694 Z= 0.307 Chirality : 0.044 0.174 2042 Planarity : 0.004 0.030 2426 Dihedral : 8.633 167.598 1902 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 1.23 (0.18), residues: 782 sheet: 0.32 (0.31), residues: 270 loop : -0.37 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.008 0.001 HIS C 266 PHE 0.022 0.001 PHE C 135 TYR 0.011 0.001 TYR D 432 ARG 0.008 0.000 ARG C 121 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 648) hydrogen bonds : angle 4.71736 ( 1857) covalent geometry : bond 0.00346 (13764) covalent geometry : angle 0.60333 (18694) *********************** 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 123 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8346 (t80) cc_final: 0.7666 (t80) REVERT: A 313 MET cc_start: 0.8168 (mpp) cc_final: 0.7858 (mpp) REVERT: B 124 LYS cc_start: 0.9400 (tmtt) cc_final: 0.9126 (tptp) REVERT: B 301 MET cc_start: 0.8494 (mmp) cc_final: 0.8272 (mmp) REVERT: C 377 MET cc_start: 0.8419 (ppp) cc_final: 0.8036 (ppp) REVERT: D 75 MET cc_start: 0.7875 (mtp) cc_final: 0.7607 (mtp) REVERT: D 124 LYS cc_start: 0.9450 (tmtt) cc_final: 0.9247 (tptp) REVERT: D 295 MET cc_start: 0.8278 (tpt) cc_final: 0.8061 (tpp) REVERT: D 299 LYS cc_start: 0.8915 (ptmm) cc_final: 0.8373 (ttpp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2769 time to fit residues: 49.2219 Evaluate side-chains 89 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 113 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.051956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.044812 restraints weight = 77303.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046120 restraints weight = 45356.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047063 restraints weight = 30873.957| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13764 Z= 0.154 Angle : 0.604 8.307 18694 Z= 0.306 Chirality : 0.044 0.162 2042 Planarity : 0.004 0.039 2426 Dihedral : 8.611 165.288 1902 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 0.65 (0.20), residues: 1684 helix: 1.21 (0.18), residues: 782 sheet: 0.30 (0.31), residues: 270 loop : -0.38 (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 0.018 0.001 PHE C 135 TYR 0.009 0.001 TYR A 224 ARG 0.007 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 648) hydrogen bonds : angle 4.72691 ( 1857) covalent geometry : bond 0.00334 (13764) covalent geometry : angle 0.60380 (18694) *********************** 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 122 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8377 (t80) cc_final: 0.7687 (t80) REVERT: A 313 MET cc_start: 0.8104 (mpp) cc_final: 0.7794 (mpp) REVERT: A 377 MET cc_start: 0.8202 (ppp) cc_final: 0.7732 (ppp) REVERT: B 124 LYS cc_start: 0.9401 (tmtt) cc_final: 0.9150 (tptp) REVERT: B 301 MET cc_start: 0.8453 (mmp) cc_final: 0.8236 (mmp) REVERT: C 377 MET cc_start: 0.8550 (ppp) cc_final: 0.8084 (ppp) REVERT: D 75 MET cc_start: 0.7852 (mtp) cc_final: 0.7587 (mtp) REVERT: D 295 MET cc_start: 0.8343 (tpt) cc_final: 0.8126 (tpp) REVERT: D 299 LYS cc_start: 0.8899 (ptmm) cc_final: 0.8343 (ttpp) REVERT: D 325 MET cc_start: 0.8657 (pmm) cc_final: 0.7961 (ptp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2696 time to fit residues: 48.0615 Evaluate side-chains 89 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 138 optimal weight: 5.9990 chunk 155 optimal weight: 0.0570 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- 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 336 GLN ** 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 = 0.3185 r_free = 0.3185 target = 0.051725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044655 restraints weight = 76746.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.045927 restraints weight = 45207.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046882 restraints weight = 30889.952| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13764 Z= 0.186 Angle : 0.628 9.067 18694 Z= 0.319 Chirality : 0.045 0.206 2042 Planarity : 0.004 0.046 2426 Dihedral : 8.655 162.934 1902 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 0.55 (0.20), residues: 1684 helix: 1.17 (0.18), residues: 782 sheet: 0.16 (0.31), residues: 268 loop : -0.44 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 21 HIS 0.008 0.001 HIS C 266 PHE 0.016 0.001 PHE C 135 TYR 0.028 0.001 TYR A 224 ARG 0.008 0.000 ARG C 121 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 648) hydrogen bonds : angle 4.78595 ( 1857) covalent geometry : bond 0.00402 (13764) covalent geometry : angle 0.62828 (18694) *********************** 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 118 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8390 (t80) cc_final: 0.7697 (t80) REVERT: A 313 MET cc_start: 0.8125 (mpp) cc_final: 0.7809 (mpp) REVERT: B 124 LYS cc_start: 0.9407 (tmtt) cc_final: 0.9161 (tptp) REVERT: B 301 MET cc_start: 0.8452 (mmp) cc_final: 0.8235 (mmp) REVERT: C 377 MET cc_start: 0.8526 (ppp) cc_final: 0.8091 (ppp) REVERT: D 75 MET cc_start: 0.7844 (mtp) cc_final: 0.7571 (mtp) REVERT: D 124 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9174 (tptp) REVERT: D 295 MET cc_start: 0.8425 (tpt) cc_final: 0.8031 (tpp) REVERT: D 299 LYS cc_start: 0.8899 (ptmm) cc_final: 0.8343 (ttpp) REVERT: D 302 MET cc_start: 0.8720 (mtm) cc_final: 0.8486 (mtm) REVERT: D 325 MET cc_start: 0.8605 (pmm) cc_final: 0.7974 (ptp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2560 time to fit residues: 44.5179 Evaluate side-chains 91 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 27 optimal weight: 0.0470 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS 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 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.052919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.045753 restraints weight = 75869.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047068 restraints weight = 44967.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048021 restraints weight = 30865.598| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13764 Z= 0.118 Angle : 0.600 9.489 18694 Z= 0.302 Chirality : 0.044 0.191 2042 Planarity : 0.003 0.038 2426 Dihedral : 8.530 159.498 1902 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % 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: 0.63 (0.20), residues: 1684 helix: 1.22 (0.18), residues: 782 sheet: 0.26 (0.30), residues: 278 loop : -0.43 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.008 0.001 HIS C 266 PHE 0.013 0.001 PHE C 135 TYR 0.023 0.001 TYR A 224 ARG 0.008 0.000 ARG C 121 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 648) hydrogen bonds : angle 4.68003 ( 1857) covalent geometry : bond 0.00258 (13764) covalent geometry : angle 0.60005 (18694) ********************** 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 120 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.8358 (t80) cc_final: 0.7544 (t80) REVERT: A 313 MET cc_start: 0.8088 (mpp) cc_final: 0.7790 (mpp) REVERT: B 124 LYS cc_start: 0.9379 (tmtt) cc_final: 0.9145 (tptp) REVERT: C 154 MET cc_start: 0.7964 (ttt) cc_final: 0.7721 (ttt) REVERT: C 377 MET cc_start: 0.8600 (ppp) cc_final: 0.8195 (ppp) REVERT: D 75 MET cc_start: 0.7866 (mtp) cc_final: 0.7618 (mtp) REVERT: D 124 LYS cc_start: 0.9411 (tmtt) cc_final: 0.9177 (tptp) REVERT: D 295 MET cc_start: 0.8370 (tpt) cc_final: 0.8128 (tpp) REVERT: D 302 MET cc_start: 0.8719 (mtm) cc_final: 0.8459 (mtm) REVERT: D 325 MET cc_start: 0.8543 (pmm) cc_final: 0.7800 (ptp) REVERT: D 336 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7650 (tp-100) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.2681 time to fit residues: 47.1074 Evaluate side-chains 94 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 133 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 228 ASN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.045545 restraints weight = 75828.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.046897 restraints weight = 44611.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047848 restraints weight = 30334.749| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13764 Z= 0.124 Angle : 0.596 8.534 18694 Z= 0.300 Chirality : 0.044 0.188 2042 Planarity : 0.003 0.039 2426 Dihedral : 8.476 156.592 1902 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: 0.63 (0.20), residues: 1684 helix: 1.25 (0.18), residues: 782 sheet: 0.25 (0.30), residues: 278 loop : -0.46 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 346 HIS 0.007 0.001 HIS C 266 PHE 0.012 0.001 PHE C 135 TYR 0.022 0.001 TYR A 224 ARG 0.006 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 648) hydrogen bonds : angle 4.66674 ( 1857) covalent geometry : bond 0.00274 (13764) covalent geometry : angle 0.59644 (18694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3618.15 seconds wall clock time: 64 minutes 28.91 seconds (3868.91 seconds total)