Starting phenix.real_space_refine on Sun Aug 24 05:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxn_27770/08_2025/8dxn_27770.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxn_27770/08_2025/8dxn_27770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dxn_27770/08_2025/8dxn_27770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxn_27770/08_2025/8dxn_27770.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxn_27770/08_2025/8dxn_27770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxn_27770/08_2025/8dxn_27770.cif" } resolution = 3.4 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= -0.001 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 11561 2.51 5 N 2760 2.21 5 O 3031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17499 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2481 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2501 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "D" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2497 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "E" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "F" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2516 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 2 Chain: "G" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2490 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain breaks: 2 Time building chain proxies: 3.67, per 1000 atoms: 0.21 Number of scatterers: 17499 At special positions: 0 Unit cell: (119.9, 117.7, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 3031 8.00 N 2760 7.00 C 11561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 293 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 115 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 308 " distance=2.03 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 293 " distance=2.03 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: 1.29 Conformation dependent library (CDL) restraints added in 666.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 72.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.738A pdb=" N GLU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.585A pdb=" N LYS A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.860A pdb=" N ASP A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.906A pdb=" N THR A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 254 removed outlier: 3.945A pdb=" N GLU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 283 removed outlier: 3.601A pdb=" N VAL A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 342 removed outlier: 3.652A pdb=" N PHE A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.767A pdb=" N GLN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 4.215A pdb=" N GLN A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.690A pdb=" N PHE A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 3.916A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.052A pdb=" N VAL B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 49 removed outlier: 5.135A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.779A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.700A pdb=" N LYS B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.519A pdb=" N ASN B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.787A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 259 through 283 Processing helix chain 'B' and resid 314 through 341 removed outlier: 3.955A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.679A pdb=" N ALA B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'C' and resid 22 through 49 removed outlier: 4.277A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 120 removed outlier: 3.680A pdb=" N TYR C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 144 Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 152 through 166 Processing helix chain 'C' and resid 168 through 175 removed outlier: 4.011A pdb=" N THR C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 250 Processing helix chain 'C' and resid 256 through 284 removed outlier: 3.976A pdb=" N MET C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 312 through 341 removed outlier: 3.908A pdb=" N PHE C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.805A pdb=" N ARG C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 378 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'D' and resid 22 through 47 removed outlier: 3.725A pdb=" N VAL D 26 " --> pdb=" O PRO D 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.814A pdb=" N TYR D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D 118 " --> pdb=" O MET D 114 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.701A pdb=" N LYS D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 126 " --> pdb=" O TRP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 126 through 143 removed outlier: 3.701A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN D 143 " --> pdb=" O MET D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.987A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.917A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 Processing helix chain 'D' and resid 259 through 283 removed outlier: 3.755A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 283 " --> pdb=" O TYR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 341 removed outlier: 3.668A pdb=" N PHE D 316 " --> pdb=" O MET D 312 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS D 318 " --> pdb=" O HIS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 359 Processing helix chain 'D' and resid 367 through 378 removed outlier: 3.883A pdb=" N ALA D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.057A pdb=" N VAL D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 removed outlier: 3.546A pdb=" N GLU D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 49 removed outlier: 3.639A pdb=" N VAL E 47 " --> pdb=" O CYS E 43 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.685A pdb=" N TYR E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 142 removed outlier: 3.623A pdb=" N VAL E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 167 removed outlier: 3.902A pdb=" N PHE E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 removed outlier: 3.902A pdb=" N THR E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 253 removed outlier: 3.658A pdb=" N GLU E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 283 removed outlier: 3.514A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 287 removed outlier: 4.116A pdb=" N VAL E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 287' Processing helix chain 'E' and resid 315 through 344 removed outlier: 3.747A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 removed outlier: 3.628A pdb=" N ARG E 355 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 removed outlier: 3.579A pdb=" N GLN E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.999A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 405 removed outlier: 3.535A pdb=" N LEU E 405 " --> pdb=" O LYS E 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 49 removed outlier: 3.770A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.813A pdb=" N TYR F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 143 removed outlier: 3.609A pdb=" N VAL F 131 " --> pdb=" O PHE F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 4.289A pdb=" N LYS F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 167 removed outlier: 4.218A pdb=" N ASP F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 Processing helix chain 'F' and resid 232 through 253 Processing helix chain 'F' and resid 256 through 283 removed outlier: 4.478A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 342 removed outlier: 3.511A pdb=" N PHE F 316 " --> pdb=" O MET F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 367 through 378 Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.870A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 405 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 22 through 48 removed outlier: 3.635A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL G 47 " --> pdb=" O CYS G 43 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET G 48 " --> pdb=" O THR G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 120 removed outlier: 3.755A pdb=" N TYR G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.751A pdb=" N LYS G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 142 removed outlier: 3.701A pdb=" N LEU G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 148 removed outlier: 4.003A pdb=" N PHE G 148 " --> pdb=" O TRP G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 165 removed outlier: 4.081A pdb=" N ILE G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.637A pdb=" N THR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 253 Processing helix chain 'G' and resid 259 through 283 removed outlier: 3.697A pdb=" N VAL G 263 " --> pdb=" O TYR G 259 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G 281 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 287 removed outlier: 3.727A pdb=" N VAL G 287 " --> pdb=" O VAL G 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 284 through 287' Processing helix chain 'G' and resid 312 through 342 removed outlier: 3.846A pdb=" N PHE G 316 " --> pdb=" O MET G 312 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LYS G 318 " --> pdb=" O HIS G 314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE G 321 " --> pdb=" O SER G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 359 Processing helix chain 'G' and resid 368 through 378 Processing helix chain 'G' and resid 379 through 381 No H-bonds generated for 'chain 'G' and resid 379 through 381' Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.810A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL G 390 " --> pdb=" O LYS G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 405 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 56 1057 hydrogen bonds defined for protein. 3141 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: 1.89 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5193 1.34 - 1.46: 3708 1.46 - 1.58: 8844 1.58 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 17969 Sorted by residual: bond pdb=" N PRO A 22 " pdb=" CD PRO A 22 " ideal model delta sigma weight residual 1.473 1.506 -0.033 1.40e-02 5.10e+03 5.71e+00 bond pdb=" N ASN E 368 " pdb=" CA ASN E 368 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" C ARG D 249 " pdb=" N LEU D 250 " ideal model delta sigma weight residual 1.332 1.317 0.016 1.40e-02 5.10e+03 1.27e+00 bond pdb=" N ASN C 368 " pdb=" CA ASN C 368 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.23e+00 bond pdb=" CB GLU D 253 " pdb=" CG GLU D 253 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 17964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 23609 1.44 - 2.88: 543 2.88 - 4.32: 85 4.32 - 5.76: 16 5.76 - 7.21: 5 Bond angle restraints: 24258 Sorted by residual: angle pdb=" C LYS B 51 " pdb=" CA LYS B 51 " pdb=" CB LYS B 51 " ideal model delta sigma weight residual 116.34 110.92 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" C ARG D 249 " pdb=" N LEU D 250 " pdb=" CA LEU D 250 " ideal model delta sigma weight residual 121.54 128.75 -7.21 1.91e+00 2.74e-01 1.42e+01 angle pdb=" N ILE E 257 " pdb=" CA ILE E 257 " pdb=" C ILE E 257 " ideal model delta sigma weight residual 113.53 110.57 2.96 9.80e-01 1.04e+00 9.15e+00 angle pdb=" C ALA B 278 " pdb=" N TYR B 279 " pdb=" CA TYR B 279 " ideal model delta sigma weight residual 121.58 115.70 5.88 1.95e+00 2.63e-01 9.08e+00 angle pdb=" C ALA A 278 " pdb=" N TYR A 279 " pdb=" CA TYR A 279 " ideal model delta sigma weight residual 122.38 117.11 5.27 1.81e+00 3.05e-01 8.48e+00 ... (remaining 24253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9412 17.98 - 35.96: 946 35.96 - 53.93: 178 53.93 - 71.91: 19 71.91 - 89.89: 27 Dihedral angle restraints: 10582 sinusoidal: 4307 harmonic: 6275 Sorted by residual: dihedral pdb=" CA ARG D 249 " pdb=" C ARG D 249 " pdb=" N LEU D 250 " pdb=" CA LEU D 250 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU C 338 " pdb=" C LEU C 338 " pdb=" N TYR C 339 " pdb=" CA TYR C 339 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PHE E 148 " pdb=" C PHE E 148 " pdb=" N PRO E 149 " pdb=" CA PRO E 149 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 10579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1679 0.030 - 0.060: 688 0.060 - 0.090: 197 0.090 - 0.119: 65 0.119 - 0.149: 18 Chirality restraints: 2647 Sorted by residual: chirality pdb=" CA ILE B 53 " pdb=" N ILE B 53 " pdb=" C ILE B 53 " pdb=" CB ILE B 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL B 26 " pdb=" N VAL B 26 " pdb=" C VAL B 26 " pdb=" CB VAL B 26 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE B 363 " pdb=" N ILE B 363 " pdb=" C ILE B 363 " pdb=" CB ILE B 363 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2644 not shown) Planarity restraints: 2955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 21 " 0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A 22 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 145 " -0.017 2.00e-02 2.50e+03 1.32e-02 4.33e+00 pdb=" CG TRP D 145 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 145 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP D 145 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 145 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 145 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 327 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C VAL A 327 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 327 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 328 " 0.011 2.00e-02 2.50e+03 ... (remaining 2952 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 501 2.71 - 3.26: 17667 3.26 - 3.81: 27495 3.81 - 4.35: 32102 4.35 - 4.90: 56504 Nonbonded interactions: 134269 Sorted by model distance: nonbonded pdb=" NE2 HIS A 134 " pdb=" OH TYR A 279 " model vdw 2.166 3.120 nonbonded pdb=" NE2 HIS G 134 " pdb=" OH TYR G 279 " model vdw 2.227 3.120 nonbonded pdb=" OH TYR D 123 " pdb=" OD1 ASN D 280 " model vdw 2.242 3.040 nonbonded pdb=" O PHE G 351 " pdb=" NE ARG G 355 " model vdw 2.248 3.120 nonbonded pdb=" NE2 HIS E 134 " pdb=" OH TYR E 279 " model vdw 2.254 3.120 ... (remaining 134264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'B' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'C' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'D' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'E' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'F' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'G' and (resid 16 through 175 or resid 177 or resid 235 through 405)) } 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: 3.150 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.470 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17983 Z= 0.147 Angle : 0.552 7.205 24286 Z= 0.313 Chirality : 0.037 0.149 2647 Planarity : 0.004 0.112 2955 Dihedral : 15.085 89.891 6478 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.69 (0.20), residues: 2059 helix: 1.69 (0.15), residues: 1346 sheet: 0.18 (0.44), residues: 136 loop : -2.60 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 58 TYR 0.020 0.001 TYR C 279 PHE 0.031 0.002 PHE F 242 TRP 0.036 0.002 TRP D 145 HIS 0.007 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00316 (17969) covalent geometry : angle 0.55205 (24258) SS BOND : bond 0.00276 ( 14) SS BOND : angle 0.45866 ( 28) hydrogen bonds : bond 0.13752 ( 1057) hydrogen bonds : angle 5.67152 ( 3141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.439 Fit side-chains REVERT: A 347 ARG cc_start: 0.7326 (ptt180) cc_final: 0.6929 (mtm180) REVERT: A 373 MET cc_start: 0.7583 (mpp) cc_final: 0.7358 (mpp) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1182 time to fit residues: 55.7451 Evaluate side-chains 262 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.0000 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.6980 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 251 HIS E 251 HIS E 288 GLN F 121 HIS ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN G 305 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.191770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149812 restraints weight = 21669.877| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.21 r_work: 0.3408 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17983 Z= 0.112 Angle : 0.496 7.442 24286 Z= 0.266 Chirality : 0.038 0.153 2647 Planarity : 0.003 0.068 2955 Dihedral : 4.110 29.101 2283 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.44 % Allowed : 9.18 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.26 (0.20), residues: 2059 helix: 2.04 (0.15), residues: 1379 sheet: 0.33 (0.45), residues: 136 loop : -2.33 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.020 0.001 TYR A 279 PHE 0.021 0.001 PHE E 273 TRP 0.018 0.001 TRP D 145 HIS 0.003 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00230 (17969) covalent geometry : angle 0.49580 (24258) SS BOND : bond 0.00141 ( 14) SS BOND : angle 0.36612 ( 28) hydrogen bonds : bond 0.04310 ( 1057) hydrogen bonds : angle 3.87187 ( 3141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.649 Fit side-chains REVERT: A 147 LYS cc_start: 0.6372 (mmmm) cc_final: 0.6150 (tttt) REVERT: A 347 ARG cc_start: 0.7395 (ptt180) cc_final: 0.6600 (mtm180) REVERT: A 373 MET cc_start: 0.7635 (mpp) cc_final: 0.7090 (mpp) REVERT: B 380 TYR cc_start: 0.7027 (t80) cc_final: 0.6615 (t80) REVERT: D 321 PHE cc_start: 0.6854 (m-80) cc_final: 0.6546 (t80) REVERT: E 143 ASN cc_start: 0.6839 (m110) cc_final: 0.6614 (m-40) REVERT: F 147 LYS cc_start: 0.8603 (ttmt) cc_final: 0.7460 (tppt) REVERT: F 357 GLU cc_start: 0.7412 (mp0) cc_final: 0.7116 (mp0) REVERT: G 48 MET cc_start: 0.8172 (ptp) cc_final: 0.7664 (ppp) REVERT: G 296 ASP cc_start: 0.8473 (t0) cc_final: 0.8212 (t0) outliers start: 28 outliers final: 21 residues processed: 301 average time/residue: 0.1372 time to fit residues: 60.3834 Evaluate side-chains 282 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 261 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 279 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 207 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 0.0980 chunk 127 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.191301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140249 restraints weight = 21964.978| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.52 r_work: 0.3376 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17983 Z= 0.105 Angle : 0.466 7.333 24286 Z= 0.250 Chirality : 0.038 0.153 2647 Planarity : 0.003 0.046 2955 Dihedral : 3.972 24.558 2283 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.86 % Allowed : 11.96 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.42 (0.20), residues: 2059 helix: 2.18 (0.15), residues: 1379 sheet: 0.44 (0.45), residues: 134 loop : -2.33 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.016 0.001 TYR C 336 PHE 0.017 0.001 PHE A 41 TRP 0.015 0.001 TRP G 340 HIS 0.003 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00225 (17969) covalent geometry : angle 0.46635 (24258) SS BOND : bond 0.00162 ( 14) SS BOND : angle 0.37993 ( 28) hydrogen bonds : bond 0.03904 ( 1057) hydrogen bonds : angle 3.58835 ( 3141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 0.500 Fit side-chains REVERT: A 147 LYS cc_start: 0.6354 (mmmm) cc_final: 0.6121 (tttt) REVERT: A 347 ARG cc_start: 0.7147 (ptt180) cc_final: 0.6488 (mtm180) REVERT: A 373 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7241 (mpp) REVERT: B 376 MET cc_start: 0.7454 (mmm) cc_final: 0.7166 (tpp) REVERT: D 37 MET cc_start: 0.7636 (mmt) cc_final: 0.7423 (mmm) REVERT: E 143 ASN cc_start: 0.6813 (m110) cc_final: 0.6434 (m-40) REVERT: F 143 ASN cc_start: 0.7403 (m-40) cc_final: 0.6338 (t0) REVERT: F 312 MET cc_start: 0.8415 (pmm) cc_final: 0.8162 (pmm) REVERT: G 45 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6309 (tt) REVERT: G 48 MET cc_start: 0.8100 (ptp) cc_final: 0.7607 (ppp) REVERT: G 296 ASP cc_start: 0.8542 (t0) cc_final: 0.8239 (t0) outliers start: 36 outliers final: 28 residues processed: 318 average time/residue: 0.1277 time to fit residues: 59.8037 Evaluate side-chains 309 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 279 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 166 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS D 107 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS E 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.189066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145942 restraints weight = 22058.038| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.44 r_work: 0.3342 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17983 Z= 0.124 Angle : 0.481 6.665 24286 Z= 0.257 Chirality : 0.038 0.140 2647 Planarity : 0.003 0.040 2955 Dihedral : 3.921 25.099 2283 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.53 % Allowed : 13.14 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.35 (0.20), residues: 2059 helix: 2.10 (0.15), residues: 1396 sheet: 0.38 (0.45), residues: 134 loop : -2.44 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 18 TYR 0.015 0.001 TYR C 279 PHE 0.020 0.001 PHE G 388 TRP 0.017 0.001 TRP B 24 HIS 0.004 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00283 (17969) covalent geometry : angle 0.48060 (24258) SS BOND : bond 0.00199 ( 14) SS BOND : angle 0.40732 ( 28) hydrogen bonds : bond 0.04169 ( 1057) hydrogen bonds : angle 3.52668 ( 3141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 147 LYS cc_start: 0.6375 (mmmm) cc_final: 0.6165 (tttt) REVERT: A 347 ARG cc_start: 0.7209 (ptt180) cc_final: 0.6411 (mtm-85) REVERT: A 373 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7372 (mpp) REVERT: B 376 MET cc_start: 0.7579 (mmm) cc_final: 0.7284 (tpp) REVERT: B 380 TYR cc_start: 0.7163 (t80) cc_final: 0.6528 (t80) REVERT: D 37 MET cc_start: 0.7730 (mmt) cc_final: 0.7490 (mmm) REVERT: D 243 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: D 373 MET cc_start: 0.7740 (tpp) cc_final: 0.7526 (tpt) REVERT: E 143 ASN cc_start: 0.6716 (m110) cc_final: 0.6503 (m-40) REVERT: E 156 GLU cc_start: 0.8369 (pt0) cc_final: 0.8073 (pt0) REVERT: F 18 ARG cc_start: 0.7564 (ptt90) cc_final: 0.7044 (ptt90) REVERT: F 143 ASN cc_start: 0.7499 (m-40) cc_final: 0.6389 (t0) REVERT: F 147 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8206 (ttmt) REVERT: F 312 MET cc_start: 0.8547 (pmm) cc_final: 0.8294 (pmm) REVERT: F 357 GLU cc_start: 0.7427 (mp0) cc_final: 0.7065 (mp0) REVERT: G 45 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6456 (tt) REVERT: G 48 MET cc_start: 0.7971 (ptp) cc_final: 0.7596 (ppp) REVERT: G 105 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8411 (tt) REVERT: G 340 TRP cc_start: 0.8129 (t60) cc_final: 0.7786 (t60) outliers start: 49 outliers final: 36 residues processed: 322 average time/residue: 0.1443 time to fit residues: 68.9769 Evaluate side-chains 319 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 298 GLN Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 174 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 251 HIS E 288 GLN F 106 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.188848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134241 restraints weight = 21875.065| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.31 r_work: 0.3356 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17983 Z= 0.122 Angle : 0.481 8.173 24286 Z= 0.256 Chirality : 0.038 0.141 2647 Planarity : 0.003 0.039 2955 Dihedral : 3.909 24.970 2283 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.53 % Allowed : 14.69 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.37 (0.20), residues: 2059 helix: 2.12 (0.15), residues: 1396 sheet: 0.36 (0.45), residues: 134 loop : -2.44 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 18 TYR 0.019 0.001 TYR F 343 PHE 0.024 0.001 PHE G 158 TRP 0.016 0.001 TRP B 24 HIS 0.004 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00279 (17969) covalent geometry : angle 0.48067 (24258) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.39639 ( 28) hydrogen bonds : bond 0.04077 ( 1057) hydrogen bonds : angle 3.48268 ( 3141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.736 Fit side-chains REVERT: A 373 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7196 (mpp) REVERT: B 376 MET cc_start: 0.7428 (mmm) cc_final: 0.7118 (tpp) REVERT: B 380 TYR cc_start: 0.7198 (t80) cc_final: 0.6608 (t80) REVERT: D 37 MET cc_start: 0.7616 (mmt) cc_final: 0.7392 (mmm) REVERT: D 243 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: E 143 ASN cc_start: 0.6724 (m110) cc_final: 0.6472 (m-40) REVERT: E 156 GLU cc_start: 0.8351 (pt0) cc_final: 0.8092 (pt0) REVERT: E 352 GLU cc_start: 0.7845 (tp30) cc_final: 0.7279 (tm-30) REVERT: F 143 ASN cc_start: 0.7374 (m-40) cc_final: 0.6271 (t0) REVERT: F 147 LYS cc_start: 0.8253 (ttmt) cc_final: 0.8007 (ttmt) REVERT: F 312 MET cc_start: 0.8431 (pmm) cc_final: 0.8129 (pmm) REVERT: G 45 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6303 (tt) REVERT: G 48 MET cc_start: 0.8005 (ptp) cc_final: 0.7575 (ppp) REVERT: G 105 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8279 (tt) REVERT: G 367 LYS cc_start: 0.6603 (pttt) cc_final: 0.6339 (pttm) REVERT: G 387 ARG cc_start: 0.4728 (mmm-85) cc_final: 0.4437 (mtp180) outliers start: 49 outliers final: 41 residues processed: 318 average time/residue: 0.1420 time to fit residues: 66.8642 Evaluate side-chains 316 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 109 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 196 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 106 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.189920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138091 restraints weight = 21825.712| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.51 r_work: 0.3355 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17983 Z= 0.110 Angle : 0.465 7.514 24286 Z= 0.248 Chirality : 0.038 0.142 2647 Planarity : 0.003 0.039 2955 Dihedral : 3.857 24.800 2283 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.63 % Allowed : 15.57 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.42 (0.20), residues: 2059 helix: 2.16 (0.15), residues: 1397 sheet: 0.36 (0.45), residues: 134 loop : -2.40 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 18 TYR 0.016 0.001 TYR F 343 PHE 0.028 0.001 PHE G 388 TRP 0.015 0.001 TRP G 170 HIS 0.003 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00245 (17969) covalent geometry : angle 0.46509 (24258) SS BOND : bond 0.00184 ( 14) SS BOND : angle 0.38713 ( 28) hydrogen bonds : bond 0.03807 ( 1057) hydrogen bonds : angle 3.40283 ( 3141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7194 (mpp) REVERT: B 376 MET cc_start: 0.7444 (mmm) cc_final: 0.7118 (tpp) REVERT: B 380 TYR cc_start: 0.7191 (t80) cc_final: 0.6591 (t80) REVERT: D 37 MET cc_start: 0.7605 (mmt) cc_final: 0.7377 (mmm) REVERT: D 243 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: E 156 GLU cc_start: 0.8293 (pt0) cc_final: 0.8062 (pt0) REVERT: F 18 ARG cc_start: 0.7589 (ptt90) cc_final: 0.7114 (ptt90) REVERT: F 143 ASN cc_start: 0.7269 (m-40) cc_final: 0.6459 (t0) REVERT: F 147 LYS cc_start: 0.8280 (ttmt) cc_final: 0.8011 (ttmt) REVERT: F 312 MET cc_start: 0.8492 (pmm) cc_final: 0.8206 (pmm) REVERT: G 48 MET cc_start: 0.8022 (ptp) cc_final: 0.7589 (ppp) REVERT: G 105 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8231 (tt) REVERT: G 367 LYS cc_start: 0.6581 (pttt) cc_final: 0.6327 (pttm) outliers start: 51 outliers final: 42 residues processed: 312 average time/residue: 0.1329 time to fit residues: 62.3553 Evaluate side-chains 312 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 3 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS E 288 GLN F 113 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.189021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145380 restraints weight = 22007.188| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.39 r_work: 0.3356 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17983 Z= 0.120 Angle : 0.486 10.777 24286 Z= 0.257 Chirality : 0.038 0.140 2647 Planarity : 0.003 0.038 2955 Dihedral : 3.873 24.878 2283 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.94 % Allowed : 15.98 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.42 (0.20), residues: 2059 helix: 2.15 (0.15), residues: 1397 sheet: 0.33 (0.45), residues: 134 loop : -2.39 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.015 0.001 TYR A 279 PHE 0.028 0.001 PHE G 388 TRP 0.015 0.001 TRP G 170 HIS 0.004 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00274 (17969) covalent geometry : angle 0.48583 (24258) SS BOND : bond 0.00217 ( 14) SS BOND : angle 0.38870 ( 28) hydrogen bonds : bond 0.03976 ( 1057) hydrogen bonds : angle 3.43034 ( 3141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 270 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7338 (mpp) REVERT: B 376 MET cc_start: 0.7558 (mmm) cc_final: 0.7211 (tpp) REVERT: B 380 TYR cc_start: 0.7252 (t80) cc_final: 0.6700 (t80) REVERT: D 37 MET cc_start: 0.7677 (mmt) cc_final: 0.7430 (mmm) REVERT: D 243 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: E 143 ASN cc_start: 0.6664 (m110) cc_final: 0.6426 (m110) REVERT: E 156 GLU cc_start: 0.8268 (pt0) cc_final: 0.7842 (pp20) REVERT: F 18 ARG cc_start: 0.7553 (ptt90) cc_final: 0.7249 (ptt90) REVERT: F 143 ASN cc_start: 0.7415 (m-40) cc_final: 0.6612 (t0) REVERT: F 312 MET cc_start: 0.8561 (pmm) cc_final: 0.8263 (pmm) REVERT: G 48 MET cc_start: 0.8108 (ptp) cc_final: 0.7808 (ppp) REVERT: G 105 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8368 (tt) REVERT: G 261 MET cc_start: 0.5448 (mmp) cc_final: 0.5073 (mtt) REVERT: G 367 LYS cc_start: 0.6661 (pttt) cc_final: 0.6400 (pttm) outliers start: 57 outliers final: 50 residues processed: 307 average time/residue: 0.1379 time to fit residues: 63.1158 Evaluate side-chains 319 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 100 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 188 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.189808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137785 restraints weight = 21931.547| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.44 r_work: 0.3361 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17983 Z= 0.111 Angle : 0.487 9.222 24286 Z= 0.258 Chirality : 0.038 0.142 2647 Planarity : 0.003 0.038 2955 Dihedral : 3.845 24.680 2283 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.04 % Allowed : 16.29 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.42 (0.20), residues: 2059 helix: 2.15 (0.15), residues: 1396 sheet: 0.33 (0.45), residues: 134 loop : -2.38 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.020 0.001 TYR F 343 PHE 0.030 0.001 PHE G 388 TRP 0.016 0.001 TRP G 170 HIS 0.003 0.000 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00247 (17969) covalent geometry : angle 0.48705 (24258) SS BOND : bond 0.00187 ( 14) SS BOND : angle 0.37895 ( 28) hydrogen bonds : bond 0.03779 ( 1057) hydrogen bonds : angle 3.39220 ( 3141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7210 (mpp) REVERT: B 376 MET cc_start: 0.7416 (mmm) cc_final: 0.7075 (tpp) REVERT: B 380 TYR cc_start: 0.7246 (t80) cc_final: 0.6612 (t80) REVERT: D 37 MET cc_start: 0.7591 (mmt) cc_final: 0.7372 (mmm) REVERT: D 243 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: E 41 PHE cc_start: 0.7739 (t80) cc_final: 0.7460 (t80) REVERT: E 143 ASN cc_start: 0.6332 (m110) cc_final: 0.6055 (m-40) REVERT: E 156 GLU cc_start: 0.8290 (pt0) cc_final: 0.7872 (pp20) REVERT: F 18 ARG cc_start: 0.7488 (ptt90) cc_final: 0.7007 (ptt90) REVERT: F 143 ASN cc_start: 0.7141 (m-40) cc_final: 0.6398 (t0) REVERT: F 312 MET cc_start: 0.8483 (pmm) cc_final: 0.8181 (pmm) REVERT: F 383 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6170 (mt) REVERT: G 48 MET cc_start: 0.8137 (ptp) cc_final: 0.7743 (ppp) REVERT: G 261 MET cc_start: 0.5392 (mmp) cc_final: 0.5021 (mtt) REVERT: G 367 LYS cc_start: 0.6600 (pttt) cc_final: 0.6361 (pttm) outliers start: 59 outliers final: 52 residues processed: 314 average time/residue: 0.1258 time to fit residues: 59.8272 Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 184 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 196 optimal weight: 0.0980 chunk 157 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.185911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145228 restraints weight = 21873.736| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.45 r_work: 0.3323 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17983 Z= 0.160 Angle : 0.534 8.794 24286 Z= 0.285 Chirality : 0.040 0.137 2647 Planarity : 0.003 0.039 2955 Dihedral : 3.996 25.657 2283 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.04 % Allowed : 16.49 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.26 (0.20), residues: 2059 helix: 2.03 (0.14), residues: 1399 sheet: 0.37 (0.46), residues: 132 loop : -2.47 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.023 0.001 TYR F 343 PHE 0.027 0.002 PHE A 41 TRP 0.016 0.001 TRP G 170 HIS 0.004 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00381 (17969) covalent geometry : angle 0.53426 (24258) SS BOND : bond 0.00268 ( 14) SS BOND : angle 0.40644 ( 28) hydrogen bonds : bond 0.04625 ( 1057) hydrogen bonds : angle 3.57756 ( 3141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 265 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: B 380 TYR cc_start: 0.7585 (t80) cc_final: 0.6863 (t80) REVERT: B 384 TYR cc_start: 0.5217 (m-80) cc_final: 0.4994 (m-80) REVERT: D 37 MET cc_start: 0.7760 (mmt) cc_final: 0.7478 (mmm) REVERT: D 243 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: E 156 GLU cc_start: 0.8331 (pt0) cc_final: 0.7849 (pp20) REVERT: F 143 ASN cc_start: 0.7649 (m-40) cc_final: 0.6664 (t0) REVERT: F 312 MET cc_start: 0.8559 (pmm) cc_final: 0.8320 (pmm) REVERT: F 383 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6339 (mt) REVERT: G 48 MET cc_start: 0.8189 (ptp) cc_final: 0.7832 (ppp) REVERT: G 105 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8543 (tt) REVERT: G 158 PHE cc_start: 0.7858 (t80) cc_final: 0.7501 (t80) REVERT: G 367 LYS cc_start: 0.6771 (pttt) cc_final: 0.6489 (pttm) outliers start: 59 outliers final: 52 residues processed: 305 average time/residue: 0.1324 time to fit residues: 61.1707 Evaluate side-chains 314 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 259 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 3.9990 chunk 188 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 chunk 193 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.188526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147015 restraints weight = 21810.436| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.34 r_work: 0.3357 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17983 Z= 0.120 Angle : 0.501 9.081 24286 Z= 0.267 Chirality : 0.038 0.142 2647 Planarity : 0.003 0.039 2955 Dihedral : 3.925 24.514 2283 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.94 % Allowed : 16.75 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.31 (0.20), residues: 2059 helix: 2.08 (0.14), residues: 1396 sheet: 0.27 (0.45), residues: 134 loop : -2.44 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 58 TYR 0.020 0.001 TYR F 343 PHE 0.028 0.001 PHE A 41 TRP 0.016 0.001 TRP G 170 HIS 0.003 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00273 (17969) covalent geometry : angle 0.50136 (24258) SS BOND : bond 0.00216 ( 14) SS BOND : angle 0.39772 ( 28) hydrogen bonds : bond 0.03974 ( 1057) hydrogen bonds : angle 3.45849 ( 3141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 272 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7444 (mtp) cc_final: 0.7191 (mtm) REVERT: B 300 MET cc_start: 0.8938 (mtm) cc_final: 0.8532 (mtp) REVERT: B 380 TYR cc_start: 0.7478 (t80) cc_final: 0.6920 (t80) REVERT: D 37 MET cc_start: 0.7748 (mmt) cc_final: 0.7494 (mmm) REVERT: D 243 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: D 312 MET cc_start: 0.8751 (ptp) cc_final: 0.8510 (ptp) REVERT: E 156 GLU cc_start: 0.8191 (pt0) cc_final: 0.7780 (pp20) REVERT: F 18 ARG cc_start: 0.7479 (ptt90) cc_final: 0.7276 (ptt90) REVERT: F 143 ASN cc_start: 0.7453 (m-40) cc_final: 0.6791 (t0) REVERT: F 248 PHE cc_start: 0.7940 (t80) cc_final: 0.7671 (t80) REVERT: F 312 MET cc_start: 0.8515 (pmm) cc_final: 0.8298 (pmm) REVERT: F 383 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6369 (mt) REVERT: G 48 MET cc_start: 0.8204 (ptp) cc_final: 0.7832 (ppp) REVERT: G 105 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8400 (tt) REVERT: G 158 PHE cc_start: 0.7976 (t80) cc_final: 0.7691 (t80) REVERT: G 367 LYS cc_start: 0.6739 (pttt) cc_final: 0.6420 (pttm) outliers start: 57 outliers final: 52 residues processed: 311 average time/residue: 0.1322 time to fit residues: 62.0003 Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 145 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 265 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 383 LEU Chi-restraints excluded: chain G residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 108 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.186456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145857 restraints weight = 21966.366| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.61 r_work: 0.3328 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17983 Z= 0.154 Angle : 0.537 9.348 24286 Z= 0.288 Chirality : 0.039 0.137 2647 Planarity : 0.003 0.039 2955 Dihedral : 4.021 25.360 2283 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.09 % Allowed : 17.11 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.20 (0.20), residues: 2059 helix: 2.00 (0.14), residues: 1397 sheet: 0.32 (0.45), residues: 132 loop : -2.54 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 118 TYR 0.022 0.001 TYR F 343 PHE 0.032 0.002 PHE E 148 TRP 0.016 0.001 TRP G 170 HIS 0.004 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00364 (17969) covalent geometry : angle 0.53752 (24258) SS BOND : bond 0.00251 ( 14) SS BOND : angle 0.39269 ( 28) hydrogen bonds : bond 0.04479 ( 1057) hydrogen bonds : angle 3.57402 ( 3141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4801.91 seconds wall clock time: 82 minutes 48.26 seconds (4968.26 seconds total)