Starting phenix.real_space_refine on Thu Aug 6 03:43:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24sv_69801/08_2026/24sv_69801.cif Found real_map, /net/cci-nas-00/data/ceres_data/24sv_69801/08_2026/24sv_69801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24sv_69801/08_2026/24sv_69801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24sv_69801/08_2026/24sv_69801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24sv_69801/08_2026/24sv_69801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24sv_69801/08_2026/24sv_69801.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 46 5.16 5 C 8280 2.51 5 N 2208 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13112 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3258 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406} Chain: "B" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3240 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 400} Chain: "C" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3258 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406} Chain: "D" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3240 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 400} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.37, per 1000 atoms: 0.26 Number of scatterers: 13112 At special positions: 0 Unit cell: (70.7764, 70.7764, 195.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 8 15.00 Mg 4 11.99 O 2566 8.00 N 2208 7.00 C 8280 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: 0.94 Conformation dependent library (CDL) restraints added in 474.5 milliseconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3088 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 8 sheets defined 50.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 29 removed outlier: 3.623A pdb=" N ALA A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.692A pdb=" N GLY A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 123 removed outlier: 3.523A pdb=" N VAL A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 157 removed outlier: 3.518A pdb=" N GLY A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.565A pdb=" N ASN A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 219 through 240 removed outlier: 3.546A pdb=" N LEU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 282 through 291 removed outlier: 3.621A pdb=" N PHE A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 320 through 333 removed outlier: 3.802A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 removed outlier: 3.684A pdb=" N PHE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.131A pdb=" N TYR A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 421 removed outlier: 3.589A pdb=" N MET A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 29 removed outlier: 3.583A pdb=" N GLN B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 48 removed outlier: 3.512A pdb=" N VAL B 48 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 48' Processing helix chain 'B' and resid 68 through 75 removed outlier: 3.611A pdb=" N LYS B 72 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 106 through 123 removed outlier: 4.282A pdb=" N TYR B 110 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLN B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 157 removed outlier: 3.572A pdb=" N GLY B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.531A pdb=" N ARG B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B 192 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 213 Processing helix chain 'B' and resid 218 through 234 Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.535A pdb=" N ARG B 238 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 Processing helix chain 'B' and resid 281 through 289 removed outlier: 3.597A pdb=" N GLU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 317 through 330 removed outlier: 3.554A pdb=" N MET B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 384 removed outlier: 3.852A pdb=" N PHE B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 removed outlier: 3.522A pdb=" N ASP B 393 " --> pdb=" O HIS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 418 removed outlier: 3.555A pdb=" N ARG B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 29 removed outlier: 3.623A pdb=" N ALA C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 78 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.692A pdb=" N GLY C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 123 removed outlier: 3.523A pdb=" N VAL C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 157 removed outlier: 3.518A pdb=" N GLY C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.565A pdb=" N ASN C 182 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS C 189 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 212 Processing helix chain 'C' and resid 219 through 240 removed outlier: 3.545A pdb=" N LEU C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 235 " --> pdb=" O MET C 231 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.621A pdb=" N PHE C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 320 through 333 removed outlier: 3.803A pdb=" N GLY C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 386 removed outlier: 3.685A pdb=" N PHE C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 removed outlier: 4.132A pdb=" N TYR C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 421 removed outlier: 3.589A pdb=" N MET C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 29 removed outlier: 3.583A pdb=" N GLN D 20 " --> pdb=" O GLN D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.512A pdb=" N VAL D 48 " --> pdb=" O ARG D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 68 through 75 removed outlier: 3.611A pdb=" N LYS D 72 " --> pdb=" O PRO D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 106 through 123 removed outlier: 4.281A pdb=" N TYR D 110 " --> pdb=" O MET D 106 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLN D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 157 removed outlier: 3.573A pdb=" N GLY D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 194 removed outlier: 3.531A pdb=" N ARG D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG D 192 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 213 Processing helix chain 'D' and resid 218 through 234 Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.534A pdb=" N ARG D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 281 through 289 removed outlier: 3.597A pdb=" N GLU D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.554A pdb=" N MET D 321 " --> pdb=" O ASN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 384 removed outlier: 3.852A pdb=" N PHE D 371 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 373 " --> pdb=" O GLN D 369 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 393 removed outlier: 3.523A pdb=" N ASP D 393 " --> pdb=" O HIS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 418 removed outlier: 3.554A pdb=" N ARG D 405 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 8.571A pdb=" N ILE A 88 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 63 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER A 136 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 196 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 197 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER A 266 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 199 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N PHE A 268 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 14.095A pdb=" N ASP A 201 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE A 263 " --> pdb=" O HIS A 367 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N HIS A 367 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR A 360 " --> pdb=" O MET A 314 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET A 314 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 362 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 312 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 364 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER A 310 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN A 366 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 53 removed outlier: 5.834A pdb=" N LYS A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 89 removed outlier: 8.623A pdb=" N VAL B 89 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 63 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU B 4 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE B 131 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 6 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL B 133 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 8 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS B 135 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL B 10 " --> pdb=" O HIS B 135 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU B 163 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE B 131 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE B 165 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 133 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE B 167 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N HIS B 135 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 196 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER B 197 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR B 265 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE B 199 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N THR B 267 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE B 262 " --> pdb=" O HIS B 364 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS B 364 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 307 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 53 Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 89 removed outlier: 8.571A pdb=" N ILE C 88 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 63 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER C 136 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 196 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR C 197 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER C 266 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL C 199 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N PHE C 268 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 14.095A pdb=" N ASP C 201 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE C 263 " --> pdb=" O HIS C 367 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N HIS C 367 " --> pdb=" O PHE C 263 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR C 360 " --> pdb=" O MET C 314 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N MET C 314 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 362 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL C 312 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 364 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER C 310 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 366 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 49 through 53 removed outlier: 5.834A pdb=" N LYS C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 88 through 89 removed outlier: 8.622A pdb=" N VAL D 89 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 63 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU D 4 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE D 131 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 6 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL D 133 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 8 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS D 135 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL D 10 " --> pdb=" O HIS D 135 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU D 163 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE D 131 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE D 165 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL D 133 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE D 167 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N HIS D 135 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS D 196 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER D 197 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR D 265 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE D 199 " --> pdb=" O THR D 265 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N THR D 267 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE D 262 " --> pdb=" O HIS D 364 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS D 364 " --> pdb=" O PHE D 262 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 307 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 50 through 53 634 hydrogen bonds defined for protein. 1872 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: 1.76 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3637 1.33 - 1.45: 2259 1.45 - 1.57: 7384 1.57 - 1.69: 12 1.69 - 1.81: 88 Bond restraints: 13380 Sorted by residual: bond pdb=" N VAL C 58 " pdb=" CA VAL C 58 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.01e-02 9.80e+03 1.02e+01 bond pdb=" N VAL A 58 " pdb=" CA VAL A 58 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.01e-02 9.80e+03 1.00e+01 bond pdb=" N LYS A 216 " pdb=" CA LYS A 216 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" N LYS C 216 " pdb=" CA LYS C 216 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 9.07e+00 bond pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.73e+00 ... (remaining 13375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 17727 2.12 - 4.24: 368 4.24 - 6.36: 58 6.36 - 8.48: 12 8.48 - 10.59: 5 Bond angle restraints: 18170 Sorted by residual: angle pdb=" N THR D 284 " pdb=" CA THR D 284 " pdb=" C THR D 284 " ideal model delta sigma weight residual 111.28 102.07 9.21 1.09e+00 8.42e-01 7.14e+01 angle pdb=" N THR B 284 " pdb=" CA THR B 284 " pdb=" C THR B 284 " ideal model delta sigma weight residual 111.28 102.07 9.21 1.09e+00 8.42e-01 7.13e+01 angle pdb=" C LYS B 283 " pdb=" CA LYS B 283 " pdb=" CB LYS B 283 " ideal model delta sigma weight residual 110.01 117.48 -7.47 1.80e+00 3.09e-01 1.72e+01 angle pdb=" C LYS D 283 " pdb=" CA LYS D 283 " pdb=" CB LYS D 283 " ideal model delta sigma weight residual 110.01 117.44 -7.43 1.80e+00 3.09e-01 1.70e+01 angle pdb=" CA LYS C 216 " pdb=" C LYS C 216 " pdb=" O LYS C 216 " ideal model delta sigma weight residual 121.00 116.86 4.14 1.05e+00 9.07e-01 1.55e+01 ... (remaining 18165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 7442 24.39 - 48.78: 424 48.78 - 73.17: 70 73.17 - 97.56: 7 97.56 - 121.95: 1 Dihedral angle restraints: 7944 sinusoidal: 3126 harmonic: 4818 Sorted by residual: dihedral pdb=" C5' GDP B 501 " pdb=" O5' GDP B 501 " pdb=" PA GDP B 501 " pdb=" O3A GDP B 501 " ideal model delta sinusoidal sigma weight residual 179.98 58.03 121.95 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" CA ALA D 268 " pdb=" C ALA D 268 " pdb=" N PRO D 269 " pdb=" CA PRO D 269 " ideal model delta harmonic sigma weight residual 0.00 -28.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ALA B 268 " pdb=" C ALA B 268 " pdb=" N PRO B 269 " pdb=" CA PRO B 269 " ideal model delta harmonic sigma weight residual 0.00 -27.97 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 7941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1456 0.042 - 0.084: 404 0.084 - 0.126: 166 0.126 - 0.168: 24 0.168 - 0.209: 8 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CA ILE B 281 " pdb=" N ILE B 281 " pdb=" C ILE B 281 " pdb=" CB ILE B 281 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE D 281 " pdb=" N ILE D 281 " pdb=" C ILE D 281 " pdb=" CB ILE D 281 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL B 58 " pdb=" N VAL B 58 " pdb=" C VAL B 58 " pdb=" CB VAL B 58 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2055 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 189 " -0.284 9.50e-02 1.11e+02 1.27e-01 1.01e+01 pdb=" NE ARG B 189 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 189 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 189 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 189 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 189 " -0.283 9.50e-02 1.11e+02 1.27e-01 1.00e+01 pdb=" NE ARG D 189 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 189 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 189 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 189 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 315 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" CG ASN B 315 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 315 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN B 315 " -0.015 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1003 2.74 - 3.28: 12910 3.28 - 3.82: 21058 3.82 - 4.36: 25804 4.36 - 4.90: 44805 Nonbonded interactions: 105580 Sorted by model distance: nonbonded pdb=" O GLY B 116 " pdb=" ND2 ASN B 120 " model vdw 2.203 3.120 nonbonded pdb=" O GLY D 116 " pdb=" ND2 ASN D 120 " model vdw 2.203 3.120 nonbonded pdb=" OG SER D 273 " pdb=" CB ASN D 353 " model vdw 2.269 3.440 nonbonded pdb=" OG SER B 273 " pdb=" CB ASN B 353 " model vdw 2.269 3.440 nonbonded pdb=" OE1 GLN B 279 " pdb=" CG LYS B 283 " model vdw 2.280 3.440 ... (remaining 105575 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 1 through 419) selection = (chain 'D' and resid 1 through 419) } 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 individual isotropic 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: 4.530 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.850 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.004 0.042 13380 Z= 0.246 Angle : 0.740 10.594 18170 Z= 0.425 Chirality : 0.047 0.209 2058 Planarity : 0.006 0.127 2340 Dihedral : 15.345 121.951 4856 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.70 % Favored : 96.06 % Rotamer: Outliers : 1.13 % Allowed : 12.38 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1674 helix: 1.06 (0.19), residues: 704 sheet: 1.43 (0.29), residues: 284 loop : -1.63 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 189 TYR 0.016 0.001 TYR C 160 PHE 0.021 0.001 PHE B 342 TRP 0.007 0.001 TRP C 22 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.25 (13380) covalent geometry : angle 0.74008 / 0.42 (18170) hydrogen bonds : bond 0.17883 / 12.31 ( 634) hydrogen bonds : angle 6.14209 / 4.32 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.294 Fit side-chains REVERT: B 189 ARG cc_start: 0.7506 (mmp-170) cc_final: 0.7288 (mpt180) REVERT: C 413 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7440 (mttm) REVERT: D 20 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6596 (tp-100) REVERT: D 51 ARG cc_start: 0.7329 (ttp80) cc_final: 0.7091 (ttp-110) REVERT: D 81 ASN cc_start: 0.6560 (m-40) cc_final: 0.6321 (m-40) REVERT: D 189 ARG cc_start: 0.7512 (mmp-170) cc_final: 0.7211 (mmt180) REVERT: D 352 ASN cc_start: 0.5926 (m110) cc_final: 0.5660 (t0) outliers start: 16 outliers final: 3 residues processed: 189 average time/residue: 0.5688 time to fit residues: 115.6307 Evaluate side-chains 143 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN B 81 ASN B 120 ASN B 244 ASN B 352 ASN C 410 ASN D 120 ASN D 244 ASN D 352 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.179223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167479 restraints weight = 10663.814| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 0.55 r_work: 0.3819 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13380 Z= 0.164 Angle : 0.641 7.749 18170 Z= 0.341 Chirality : 0.047 0.170 2058 Planarity : 0.005 0.045 2340 Dihedral : 7.512 91.874 1839 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.99 % Favored : 96.89 % Rotamer: Outliers : 2.39 % Allowed : 12.73 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1674 helix: 1.65 (0.19), residues: 716 sheet: 2.02 (0.29), residues: 260 loop : -1.42 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 387 TYR 0.011 0.001 TYR C 86 PHE 0.011 0.002 PHE C 340 TRP 0.006 0.001 TRP A 22 HIS 0.005 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (13380) covalent geometry : angle 0.64143 / 0.34 (18170) hydrogen bonds : bond 0.07103 / 4.75 ( 634) hydrogen bonds : angle 4.79045 / 3.37 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.312 Fit side-chains REVERT: A 151 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8178 (ttmp) REVERT: A 418 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: B 1 MET cc_start: 0.2719 (tpp) cc_final: 0.2467 (tpt) REVERT: B 121 GLU cc_start: 0.7607 (tp30) cc_final: 0.7283 (tp30) REVERT: B 123 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: B 354 MET cc_start: 0.7165 (mtt) cc_final: 0.6840 (mtt) REVERT: B 396 LEU cc_start: 0.8214 (mp) cc_final: 0.8001 (mt) REVERT: C 129 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7722 (mm110) REVERT: C 151 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8181 (ttmp) REVERT: C 200 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7707 (mt) REVERT: D 1 MET cc_start: 0.2866 (tpp) cc_final: 0.2303 (tpt) REVERT: D 51 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7388 (ttp-110) REVERT: D 81 ASN cc_start: 0.7084 (m-40) cc_final: 0.6877 (m-40) REVERT: D 123 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: D 189 ARG cc_start: 0.7979 (mmp-170) cc_final: 0.7410 (mpt180) REVERT: D 245 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7148 (tt) REVERT: D 326 ARG cc_start: 0.6748 (mtt180) cc_final: 0.6386 (mpt180) outliers start: 34 outliers final: 11 residues processed: 191 average time/residue: 0.5126 time to fit residues: 105.9198 Evaluate side-chains 152 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 GLN B 81 ASN B 120 ASN C 110 ASN C 380 GLN C 410 ASN D 120 ASN D 244 ASN D 299 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.183300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.171434 restraints weight = 10782.280| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 0.58 r_work: 0.3865 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13380 Z= 0.122 Angle : 0.544 7.477 18170 Z= 0.284 Chirality : 0.044 0.147 2058 Planarity : 0.004 0.044 2340 Dihedral : 6.764 90.284 1834 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.87 % Favored : 97.01 % Rotamer: Outliers : 2.81 % Allowed : 13.15 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1674 helix: 1.89 (0.19), residues: 728 sheet: 2.15 (0.29), residues: 260 loop : -1.31 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 60 TYR 0.006 0.001 TYR C 86 PHE 0.008 0.001 PHE D 276 TRP 0.006 0.001 TRP A 22 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (13380) covalent geometry : angle 0.54443 / 0.28 (18170) hydrogen bonds : bond 0.05273 / 3.51 ( 634) hydrogen bonds : angle 4.37776 / 3.10 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.321 Fit side-chains REVERT: A 418 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: B 38 THR cc_start: 0.5351 (OUTLIER) cc_final: 0.4820 (p) REVERT: B 123 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: B 177 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6929 (mm) REVERT: B 354 MET cc_start: 0.7182 (mtt) cc_final: 0.6724 (mtt) REVERT: B 396 LEU cc_start: 0.8156 (mp) cc_final: 0.7951 (mt) REVERT: B 399 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6196 (pt0) REVERT: C 50 LYS cc_start: 0.7648 (tttm) cc_final: 0.7375 (ttpm) REVERT: C 200 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7735 (mt) REVERT: C 288 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7343 (m110) REVERT: C 410 ASN cc_start: 0.7910 (t0) cc_final: 0.7635 (t160) REVERT: D 1 MET cc_start: 0.2718 (tpp) cc_final: 0.1766 (tpt) REVERT: D 51 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7375 (ttp-110) REVERT: D 121 GLU cc_start: 0.7646 (tp30) cc_final: 0.7403 (tp30) REVERT: D 123 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: D 245 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7153 (tt) REVERT: D 326 ARG cc_start: 0.6771 (mtt180) cc_final: 0.6381 (mpt180) REVERT: D 415 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.5600 (t80) outliers start: 40 outliers final: 6 residues processed: 190 average time/residue: 0.5116 time to fit residues: 105.6736 Evaluate side-chains 151 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain D residue 415 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 17 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 380 GLN A 410 ASN B 27 GLN B 81 ASN B 120 ASN C 16 GLN C 110 ASN C 380 GLN D 120 ASN D 299 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167191 restraints weight = 10742.711| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 0.59 r_work: 0.3811 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13380 Z= 0.156 Angle : 0.607 7.417 18170 Z= 0.321 Chirality : 0.046 0.158 2058 Planarity : 0.004 0.044 2340 Dihedral : 7.119 92.851 1832 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.99 % Favored : 96.89 % Rotamer: Outliers : 3.23 % Allowed : 13.92 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1674 helix: 1.78 (0.19), residues: 722 sheet: 2.11 (0.29), residues: 260 loop : -1.44 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.008 0.001 TYR C 86 PHE 0.011 0.002 PHE D 276 TRP 0.007 0.001 TRP A 22 HIS 0.005 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (13380) covalent geometry : angle 0.60662 / 0.32 (18170) hydrogen bonds : bond 0.06744 / 4.49 ( 634) hydrogen bonds : angle 4.60273 / 3.23 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8298 (mptm) REVERT: A 297 MET cc_start: 0.8317 (mtp) cc_final: 0.8107 (mtt) REVERT: A 418 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: B 1 MET cc_start: 0.2386 (tpt) cc_final: 0.1528 (mmm) REVERT: B 38 THR cc_start: 0.5290 (OUTLIER) cc_final: 0.4843 (t) REVERT: B 109 GLN cc_start: 0.6038 (mp10) cc_final: 0.5835 (mp10) REVERT: B 123 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: B 177 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7128 (mm) REVERT: B 354 MET cc_start: 0.7264 (mtt) cc_final: 0.6700 (mtt) REVERT: B 399 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6380 (pt0) REVERT: C 50 LYS cc_start: 0.7658 (tttm) cc_final: 0.7383 (ttpm) REVERT: C 151 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8179 (ttmp) REVERT: C 200 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7800 (mt) REVERT: C 241 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7486 (pptt) REVERT: C 288 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7411 (m110) REVERT: C 410 ASN cc_start: 0.7955 (t0) cc_final: 0.7709 (t160) REVERT: D 1 MET cc_start: 0.2982 (tpp) cc_final: 0.1996 (tpt) REVERT: D 51 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7421 (ttp-110) REVERT: D 121 GLU cc_start: 0.7742 (tp30) cc_final: 0.7451 (tp30) REVERT: D 123 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: D 177 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.6989 (mm) REVERT: D 245 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7328 (tt) REVERT: D 326 ARG cc_start: 0.6863 (mtt180) cc_final: 0.6413 (mpt180) REVERT: D 416 GLU cc_start: 0.7217 (mt-10) cc_final: 0.7003 (mt-10) outliers start: 46 outliers final: 21 residues processed: 188 average time/residue: 0.5334 time to fit residues: 109.2070 Evaluate side-chains 178 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 400 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 95 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 GLN A 410 ASN B 81 ASN B 120 ASN C 16 GLN C 110 ASN C 380 GLN D 120 ASN D 151 GLN D 299 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167184 restraints weight = 10754.296| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 0.59 r_work: 0.3814 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13380 Z= 0.154 Angle : 0.605 7.399 18170 Z= 0.320 Chirality : 0.046 0.163 2058 Planarity : 0.004 0.044 2340 Dihedral : 7.132 92.679 1832 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 3.59 % Allowed : 13.99 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1674 helix: 1.76 (0.18), residues: 722 sheet: 2.10 (0.30), residues: 260 loop : -1.48 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.009 0.001 TYR C 86 PHE 0.011 0.002 PHE D 276 TRP 0.007 0.001 TRP A 22 HIS 0.005 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (13380) covalent geometry : angle 0.60501 / 0.32 (18170) hydrogen bonds : bond 0.06663 / 4.44 ( 634) hydrogen bonds : angle 4.58824 / 3.22 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8294 (mptm) REVERT: A 418 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: B 38 THR cc_start: 0.5178 (OUTLIER) cc_final: 0.4747 (t) REVERT: B 123 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: B 177 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7142 (mm) REVERT: B 354 MET cc_start: 0.7324 (mtt) cc_final: 0.6774 (mtt) REVERT: C 50 LYS cc_start: 0.7716 (tttm) cc_final: 0.7464 (tmmt) REVERT: C 151 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8095 (ttmp) REVERT: C 200 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7746 (mt) REVERT: C 241 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7502 (pptt) REVERT: C 288 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7408 (m110) REVERT: C 410 ASN cc_start: 0.7964 (t0) cc_final: 0.7745 (t160) REVERT: D 119 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7322 (mmtp) REVERT: D 121 GLU cc_start: 0.7712 (tp30) cc_final: 0.7415 (tp30) REVERT: D 123 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: D 177 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7016 (mm) REVERT: D 245 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7257 (tt) REVERT: D 326 ARG cc_start: 0.6820 (mtt180) cc_final: 0.6417 (mpt180) REVERT: D 416 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7053 (mt-10) outliers start: 51 outliers final: 24 residues processed: 194 average time/residue: 0.5148 time to fit residues: 108.6996 Evaluate side-chains 185 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 400 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 97 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 71 optimal weight: 0.0060 chunk 157 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 51 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 380 GLN B 81 ASN B 120 ASN C 16 GLN C 110 ASN C 380 GLN D 120 ASN D 299 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.185956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.174486 restraints weight = 10695.748| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 0.55 r_work: 0.3914 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13380 Z= 0.107 Angle : 0.509 7.332 18170 Z= 0.263 Chirality : 0.043 0.143 2058 Planarity : 0.003 0.040 2340 Dihedral : 6.529 89.065 1832 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.57 % Favored : 97.25 % Rotamer: Outliers : 3.38 % Allowed : 14.21 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1674 helix: 2.12 (0.19), residues: 730 sheet: 2.00 (0.29), residues: 272 loop : -1.27 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 60 TYR 0.007 0.001 TYR D 110 PHE 0.007 0.001 PHE B 145 TRP 0.007 0.001 TRP A 22 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (13380) covalent geometry : angle 0.50853 / 0.26 (18170) hydrogen bonds : bond 0.04478 / 2.97 ( 634) hydrogen bonds : angle 4.17761 / 2.96 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 116 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7529 (mtmm) REVERT: A 271 ILE cc_start: 0.6888 (mm) cc_final: 0.6678 (mt) REVERT: A 418 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: B 1 MET cc_start: 0.2448 (tpt) cc_final: 0.1511 (mmm) REVERT: B 38 THR cc_start: 0.5109 (OUTLIER) cc_final: 0.4584 (p) REVERT: B 119 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7245 (mmtp) REVERT: B 123 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: B 177 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6890 (mm) REVERT: B 354 MET cc_start: 0.7226 (mtt) cc_final: 0.6732 (mtt) REVERT: B 399 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6201 (pt0) REVERT: B 415 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.5681 (t80) REVERT: C 50 LYS cc_start: 0.7643 (tttm) cc_final: 0.7439 (tmmt) REVERT: C 151 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8023 (ttmp) REVERT: C 200 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7641 (mt) REVERT: C 241 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7416 (pptt) REVERT: C 410 ASN cc_start: 0.7917 (t0) cc_final: 0.7661 (t160) REVERT: D 1 MET cc_start: 0.2955 (mmm) cc_final: 0.1635 (tpt) REVERT: D 20 GLN cc_start: 0.7493 (mm110) cc_final: 0.7255 (tp-100) REVERT: D 51 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7425 (ttp-110) REVERT: D 119 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7249 (mmtp) REVERT: D 121 GLU cc_start: 0.7529 (tp30) cc_final: 0.7317 (tp30) REVERT: D 123 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: D 326 ARG cc_start: 0.6762 (mtt180) cc_final: 0.6452 (mpt180) REVERT: D 353 ASN cc_start: 0.6911 (m-40) cc_final: 0.6656 (m110) REVERT: D 415 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.5551 (t80) REVERT: D 416 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6852 (mt-10) outliers start: 48 outliers final: 14 residues processed: 204 average time/residue: 0.5002 time to fit residues: 111.3500 Evaluate side-chains 181 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 415 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 65 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 8 optimal weight: 0.0270 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 380 GLN B 81 ASN B 120 ASN B 151 GLN C 110 ASN C 380 GLN D 120 ASN D 299 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.176694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165360 restraints weight = 10518.215| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.54 r_work: 0.3804 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13380 Z= 0.189 Angle : 0.671 8.247 18170 Z= 0.355 Chirality : 0.049 0.174 2058 Planarity : 0.004 0.044 2340 Dihedral : 7.407 95.102 1832 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.11 % Favored : 96.71 % Rotamer: Outliers : 3.16 % Allowed : 15.12 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1674 helix: 1.71 (0.19), residues: 724 sheet: 1.98 (0.30), residues: 262 loop : -1.48 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 56 TYR 0.010 0.001 TYR B 57 PHE 0.015 0.002 PHE C 340 TRP 0.006 0.001 TRP A 22 HIS 0.006 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (13380) covalent geometry : angle 0.67095 / 0.36 (18170) hydrogen bonds : bond 0.07836 / 5.23 ( 634) hydrogen bonds : angle 4.77187 / 3.34 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 339 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5875 (pm20) REVERT: A 418 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: B 38 THR cc_start: 0.5103 (OUTLIER) cc_final: 0.4694 (t) REVERT: B 119 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7244 (mmtp) REVERT: B 123 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: B 177 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7149 (mm) REVERT: B 354 MET cc_start: 0.7423 (mtt) cc_final: 0.6911 (mtt) REVERT: C 103 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6902 (mpp-170) REVERT: C 151 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8177 (ttmp) REVERT: C 200 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7835 (mt) REVERT: C 241 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7412 (pptt) REVERT: C 250 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7773 (mt-10) REVERT: D 1 MET cc_start: 0.2890 (mmm) cc_final: 0.1539 (tpt) REVERT: D 20 GLN cc_start: 0.7634 (mm110) cc_final: 0.7333 (tp-100) REVERT: D 119 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7311 (mmtp) REVERT: D 123 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: D 326 ARG cc_start: 0.6820 (mtt180) cc_final: 0.6478 (mpt180) REVERT: D 353 ASN cc_start: 0.7116 (m-40) cc_final: 0.6797 (m110) outliers start: 45 outliers final: 20 residues processed: 192 average time/residue: 0.5624 time to fit residues: 116.9995 Evaluate side-chains 184 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 158 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 380 GLN B 81 ASN B 120 ASN C 16 GLN C 110 ASN C 380 GLN C 410 ASN D 120 ASN D 299 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.181701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.169586 restraints weight = 10576.818| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 0.57 r_work: 0.3863 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13380 Z= 0.126 Angle : 0.552 6.769 18170 Z= 0.288 Chirality : 0.044 0.147 2058 Planarity : 0.004 0.041 2340 Dihedral : 6.888 92.376 1832 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.75 % Favored : 97.01 % Rotamer: Outliers : 3.16 % Allowed : 15.61 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1674 helix: 1.91 (0.19), residues: 730 sheet: 1.90 (0.29), residues: 276 loop : -1.43 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.008 0.001 TYR B 57 PHE 0.009 0.001 PHE A 340 TRP 0.008 0.001 TRP A 22 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (13380) covalent geometry : angle 0.55203 / 0.29 (18170) hydrogen bonds : bond 0.05530 / 3.68 ( 634) hydrogen bonds : angle 4.39646 / 3.10 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 418 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: B 1 MET cc_start: 0.2558 (tpt) cc_final: 0.1559 (mmm) REVERT: B 38 THR cc_start: 0.5092 (OUTLIER) cc_final: 0.4530 (p) REVERT: B 109 GLN cc_start: 0.5722 (mp10) cc_final: 0.5520 (mp10) REVERT: B 119 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7176 (mmtp) REVERT: B 123 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: B 177 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7041 (mm) REVERT: B 354 MET cc_start: 0.7399 (mtt) cc_final: 0.6859 (mtt) REVERT: B 399 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6241 (pt0) REVERT: C 151 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8068 (ttmp) REVERT: C 200 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7722 (mt) REVERT: C 241 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7343 (pptt) REVERT: D 1 MET cc_start: 0.2971 (mmm) cc_final: 0.1462 (tpt) REVERT: D 20 GLN cc_start: 0.7568 (mm110) cc_final: 0.7245 (tp-100) REVERT: D 38 THR cc_start: 0.5156 (OUTLIER) cc_final: 0.4946 (t) REVERT: D 51 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7473 (ttp-110) REVERT: D 119 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7228 (mmtp) REVERT: D 123 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: D 326 ARG cc_start: 0.6783 (mtt180) cc_final: 0.6503 (mpt180) REVERT: D 353 ASN cc_start: 0.7054 (m-40) cc_final: 0.6766 (m110) outliers start: 45 outliers final: 20 residues processed: 188 average time/residue: 0.5694 time to fit residues: 115.9281 Evaluate side-chains 180 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 38 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 35 optimal weight: 0.0570 chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 GLN B 81 ASN B 120 ASN C 16 GLN C 110 ASN C 380 GLN D 120 ASN D 299 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.183823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171854 restraints weight = 10682.881| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 0.57 r_work: 0.3885 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13380 Z= 0.115 Angle : 0.529 6.698 18170 Z= 0.273 Chirality : 0.043 0.157 2058 Planarity : 0.004 0.040 2340 Dihedral : 6.692 96.781 1832 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.81 % Favored : 96.95 % Rotamer: Outliers : 2.74 % Allowed : 16.24 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1674 helix: 2.09 (0.19), residues: 732 sheet: 1.98 (0.29), residues: 272 loop : -1.37 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.006 0.001 TYR D 110 PHE 0.008 0.001 PHE C 381 TRP 0.008 0.001 TRP A 22 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 (13380) covalent geometry : angle 0.52875 / 0.27 (18170) hydrogen bonds : bond 0.04936 / 3.29 ( 634) hydrogen bonds : angle 4.22980 / 2.99 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.378 Fit side-chains REVERT: A 39 ASP cc_start: 0.6650 (t70) cc_final: 0.6417 (t70) REVERT: A 116 LYS cc_start: 0.7785 (tmmt) cc_final: 0.7537 (mtmm) REVERT: A 151 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8117 (ttmp) REVERT: B 1 MET cc_start: 0.2753 (tpt) cc_final: 0.1727 (mmm) REVERT: B 38 THR cc_start: 0.4973 (OUTLIER) cc_final: 0.4425 (p) REVERT: B 119 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7211 (mmtp) REVERT: B 123 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: B 177 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6969 (mm) REVERT: B 354 MET cc_start: 0.7384 (mtt) cc_final: 0.6906 (mtt) REVERT: B 399 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6259 (pt0) REVERT: B 415 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.5644 (t80) REVERT: C 39 ASP cc_start: 0.6624 (t70) cc_final: 0.6414 (t70) REVERT: C 50 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7580 (mtmm) REVERT: C 151 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8018 (ttmp) REVERT: C 172 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6432 (mt) REVERT: C 200 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7711 (mt) REVERT: C 241 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7388 (pptt) REVERT: C 409 GLU cc_start: 0.6880 (pp20) cc_final: 0.6441 (pt0) REVERT: D 1 MET cc_start: 0.2853 (mmm) cc_final: 0.1366 (tpt) REVERT: D 20 GLN cc_start: 0.7527 (mm110) cc_final: 0.7253 (tp-100) REVERT: D 51 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7478 (ttp-110) REVERT: D 119 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7217 (mmtp) REVERT: D 123 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: D 326 ARG cc_start: 0.6777 (mtt180) cc_final: 0.6468 (mpt180) REVERT: D 353 ASN cc_start: 0.7099 (m-40) cc_final: 0.6817 (m110) REVERT: D 415 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.5609 (t80) outliers start: 39 outliers final: 17 residues processed: 189 average time/residue: 0.5516 time to fit residues: 113.1363 Evaluate side-chains 180 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 415 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 116 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 8 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 126 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 GLN B 81 ASN B 120 ASN C 16 GLN C 110 ASN C 380 GLN C 410 ASN D 120 ASN D 211 ASN D 299 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.186200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.174360 restraints weight = 10648.270| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 0.56 r_work: 0.3926 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13380 Z= 0.106 Angle : 0.510 6.957 18170 Z= 0.261 Chirality : 0.043 0.144 2058 Planarity : 0.003 0.039 2340 Dihedral : 6.453 92.336 1832 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.33 % Favored : 97.43 % Rotamer: Outliers : 2.46 % Allowed : 16.46 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1674 helix: 2.23 (0.19), residues: 732 sheet: 1.99 (0.29), residues: 272 loop : -1.28 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 103 TYR 0.006 0.001 TYR A 418 PHE 0.008 0.001 PHE B 312 TRP 0.008 0.001 TRP A 22 HIS 0.002 0.001 HIS D 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.11 (13380) covalent geometry : angle 0.50980 / 0.26 (18170) hydrogen bonds : bond 0.04446 / 2.96 ( 634) hydrogen bonds : angle 4.10402 / 2.91 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.313 Fit side-chains REVERT: A 116 LYS cc_start: 0.7755 (tmmt) cc_final: 0.7489 (mtmm) REVERT: A 151 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8094 (ttmp) REVERT: A 339 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5771 (pm20) REVERT: B 1 MET cc_start: 0.2640 (tpt) cc_final: 0.1703 (mmm) REVERT: B 38 THR cc_start: 0.4890 (OUTLIER) cc_final: 0.4320 (p) REVERT: B 119 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6953 (mmtp) REVERT: B 123 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: B 177 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6983 (mm) REVERT: B 354 MET cc_start: 0.7296 (mtt) cc_final: 0.6792 (mtt) REVERT: B 399 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6204 (pt0) REVERT: C 39 ASP cc_start: 0.6641 (t70) cc_final: 0.6407 (t70) REVERT: C 50 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7604 (mtmm) REVERT: C 151 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8007 (ttmp) REVERT: C 172 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6348 (mt) REVERT: C 200 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7602 (mt) REVERT: C 241 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7373 (pptt) REVERT: C 339 GLU cc_start: 0.6263 (pm20) cc_final: 0.5580 (tp30) REVERT: C 409 GLU cc_start: 0.6848 (pp20) cc_final: 0.6405 (pt0) REVERT: D 1 MET cc_start: 0.2834 (mmm) cc_final: 0.1255 (tpt) REVERT: D 20 GLN cc_start: 0.7381 (mm110) cc_final: 0.7150 (tp-100) REVERT: D 119 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7207 (mmtp) REVERT: D 123 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: D 326 ARG cc_start: 0.6794 (mtt180) cc_final: 0.6454 (mpt180) REVERT: D 353 ASN cc_start: 0.7085 (m-40) cc_final: 0.6794 (m110) REVERT: D 415 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.5638 (t80) outliers start: 35 outliers final: 17 residues processed: 183 average time/residue: 0.5386 time to fit residues: 106.7775 Evaluate side-chains 177 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 415 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 90 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 380 GLN B 81 ASN B 120 ASN C 110 ASN C 380 GLN D 120 ASN D 299 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.175392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.163171 restraints weight = 10594.674| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 0.59 r_work: 0.3766 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13380 Z= 0.214 Angle : 0.733 8.767 18170 Z= 0.386 Chirality : 0.051 0.195 2058 Planarity : 0.005 0.044 2340 Dihedral : 7.599 97.696 1832 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.81 % Favored : 96.95 % Rotamer: Outliers : 2.74 % Allowed : 16.74 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1674 helix: 1.49 (0.18), residues: 734 sheet: 1.93 (0.30), residues: 262 loop : -1.51 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 103 TYR 0.011 0.002 TYR B 57 PHE 0.017 0.003 PHE B 276 TRP 0.007 0.002 TRP A 229 HIS 0.007 0.002 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (13380) covalent geometry : angle 0.73269 / 0.39 (18170) hydrogen bonds : bond 0.08563 / 5.72 ( 634) hydrogen bonds : angle 4.90456 / 3.43 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3789.35 seconds wall clock time: 65 minutes 20.88 seconds (3920.88 seconds total)