Starting phenix.real_space_refine on Sun Jun 15 12:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxn_27770/06_2025/8dxn_27770.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxn_27770/06_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_27770/06_2025/8dxn_27770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxn_27770/06_2025/8dxn_27770.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxn_27770/06_2025/8dxn_27770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxn_27770/06_2025/8dxn_27770.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.89, per 1000 atoms: 0.57 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: 3.89 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.43 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: 4.74 Time building geometry restraints manager: 4.70 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 36.480 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.210 ------------------------------------------------------------------------------- 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 : 5.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 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 TRP 0.036 0.002 TRP D 145 HIS 0.007 0.001 HIS C 310 PHE 0.031 0.002 PHE F 242 TYR 0.020 0.001 TYR C 279 ARG 0.004 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.13752 ( 1057) hydrogen bonds : angle 5.67152 ( 3141) SS BOND : bond 0.00276 ( 14) SS BOND : angle 0.45866 ( 28) covalent geometry : bond 0.00316 (17969) covalent geometry : angle 0.55205 (24258) *********************** 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 : 1.769 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: 0.3016 time to fit residues: 141.3092 Evaluate side-chains 261 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 113 GLN F 121 HIS F 265 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN G 305 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.186214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143479 restraints weight = 22042.641| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.58 r_work: 0.3298 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17983 Z= 0.183 Angle : 0.564 7.202 24286 Z= 0.305 Chirality : 0.041 0.149 2647 Planarity : 0.004 0.059 2955 Dihedral : 4.302 29.601 2283 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.70 % Allowed : 10.67 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 2059 helix: 1.84 (0.15), residues: 1381 sheet: 0.12 (0.45), residues: 136 loop : -2.48 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 145 HIS 0.006 0.001 HIS C 310 PHE 0.024 0.002 PHE E 273 TYR 0.020 0.002 TYR C 279 ARG 0.003 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.05256 ( 1057) hydrogen bonds : angle 4.08560 ( 3141) SS BOND : bond 0.00271 ( 14) SS BOND : angle 0.45469 ( 28) covalent geometry : bond 0.00433 (17969) covalent geometry : angle 0.56451 (24258) *********************** 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 315 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: A 147 LYS cc_start: 0.6463 (mmmm) cc_final: 0.6210 (tttt) REVERT: A 347 ARG cc_start: 0.7308 (ptt180) cc_final: 0.6533 (mtm-85) REVERT: A 373 MET cc_start: 0.7601 (mpp) cc_final: 0.6965 (mpp) REVERT: B 380 TYR cc_start: 0.7137 (t80) cc_final: 0.6636 (t80) REVERT: F 147 LYS cc_start: 0.8590 (ttmt) cc_final: 0.7428 (tppt) REVERT: F 357 GLU cc_start: 0.7312 (mp0) cc_final: 0.7028 (mp0) REVERT: G 48 MET cc_start: 0.8333 (ptp) cc_final: 0.7813 (ppp) outliers start: 33 outliers final: 28 residues processed: 302 average time/residue: 0.3180 time to fit residues: 141.0828 Evaluate side-chains 294 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 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 43 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 312 MET 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 33 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 370 PHE Chi-restraints excluded: chain G residue 241 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 198 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 E 288 GLN ** F 106 GLN ** 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 = 0.4113 r_free = 0.4113 target = 0.187196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135454 restraints weight = 21840.720| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.54 r_work: 0.3322 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17983 Z= 0.138 Angle : 0.500 6.833 24286 Z= 0.269 Chirality : 0.039 0.146 2647 Planarity : 0.003 0.041 2955 Dihedral : 4.152 25.359 2283 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.11 % Allowed : 13.09 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 2059 helix: 2.00 (0.15), residues: 1380 sheet: 0.15 (0.46), residues: 136 loop : -2.41 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 145 HIS 0.004 0.001 HIS C 310 PHE 0.018 0.001 PHE G 388 TYR 0.017 0.001 TYR F 349 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 1057) hydrogen bonds : angle 3.74577 ( 3141) SS BOND : bond 0.00238 ( 14) SS BOND : angle 0.41969 ( 28) covalent geometry : bond 0.00316 (17969) covalent geometry : angle 0.50007 (24258) *********************** 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 324 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: A 147 LYS cc_start: 0.6516 (mmmm) cc_final: 0.6278 (tttt) REVERT: A 373 MET cc_start: 0.7632 (mpp) cc_final: 0.7154 (mpp) REVERT: D 37 MET cc_start: 0.7627 (mmt) cc_final: 0.7389 (mmm) REVERT: D 253 GLU cc_start: 0.6103 (tm-30) cc_final: 0.5843 (tm-30) REVERT: F 143 ASN cc_start: 0.7692 (m-40) cc_final: 0.6619 (t0) REVERT: F 147 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7225 (tppt) REVERT: G 48 MET cc_start: 0.8183 (ptp) cc_final: 0.7674 (ppp) REVERT: G 340 TRP cc_start: 0.8019 (t60) cc_final: 0.7699 (t60) outliers start: 41 outliers final: 35 residues processed: 308 average time/residue: 0.3159 time to fit residues: 142.6850 Evaluate side-chains 303 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 268 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU 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 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 40 VAL 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 250 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain E residue 126 TYR 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 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 277 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU 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 36 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 128 optimal weight: 0.0870 chunk 12 optimal weight: 0.2980 overall best weight: 0.8762 ------------------------------------------------------------------------------- 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 251 HIS E 288 GLN F 106 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.187076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132435 restraints weight = 21878.739| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.26 r_work: 0.3346 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1842 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= 0.132 Angle : 0.491 6.524 24286 Z= 0.264 Chirality : 0.039 0.197 2647 Planarity : 0.003 0.040 2955 Dihedral : 4.049 25.210 2283 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.14 % Allowed : 14.59 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 2059 helix: 1.97 (0.15), residues: 1398 sheet: 0.15 (0.45), residues: 136 loop : -2.48 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 145 HIS 0.004 0.001 HIS C 310 PHE 0.021 0.001 PHE G 388 TYR 0.016 0.001 TYR C 279 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 1057) hydrogen bonds : angle 3.59726 ( 3141) SS BOND : bond 0.00224 ( 14) SS BOND : angle 0.40933 ( 28) covalent geometry : bond 0.00303 (17969) covalent geometry : angle 0.49083 (24258) *********************** 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 352 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 291 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7373 (mtp) REVERT: B 380 TYR cc_start: 0.7127 (t80) cc_final: 0.6565 (t80) REVERT: B 391 PHE cc_start: 0.6346 (m-80) cc_final: 0.6112 (m-80) REVERT: C 378 ASP cc_start: 0.8032 (t0) cc_final: 0.7803 (t0) REVERT: D 37 MET cc_start: 0.7660 (mmt) cc_final: 0.7421 (mmm) REVERT: D 243 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: D 249 ARG cc_start: 0.7326 (ptm160) cc_final: 0.7101 (ptm160) REVERT: D 253 GLU cc_start: 0.6117 (tm-30) cc_final: 0.5781 (tm-30) REVERT: F 143 ASN cc_start: 0.7618 (m-40) cc_final: 0.6540 (t0) REVERT: F 147 LYS cc_start: 0.8376 (ttmt) cc_final: 0.7195 (tppt) REVERT: G 45 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6253 (tt) REVERT: G 48 MET cc_start: 0.8244 (ptp) cc_final: 0.7721 (ppp) REVERT: G 105 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8391 (tt) REVERT: G 261 MET cc_start: 0.5480 (mmp) cc_final: 0.5062 (mtt) outliers start: 61 outliers final: 46 residues processed: 327 average time/residue: 0.3840 time to fit residues: 184.6853 Evaluate side-chains 324 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE 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 373 MET 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 145 TRP Chi-restraints excluded: chain B residue 248 PHE 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 37 MET Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 268 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 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 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 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 290 THR 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 0 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 198 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 46 GLN C 49 GLN C 251 HIS E 49 GLN E 251 HIS E 288 GLN F 265 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN G 298 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141019 restraints weight = 22291.027| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.92 r_work: 0.3241 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17983 Z= 0.242 Angle : 0.605 7.840 24286 Z= 0.325 Chirality : 0.043 0.154 2647 Planarity : 0.004 0.040 2955 Dihedral : 4.340 26.445 2283 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.87 % Allowed : 15.77 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 2059 helix: 1.66 (0.14), residues: 1406 sheet: -0.06 (0.45), residues: 134 loop : -2.67 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 145 HIS 0.006 0.001 HIS C 310 PHE 0.023 0.002 PHE G 388 TYR 0.024 0.002 TYR C 279 ARG 0.004 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.05840 ( 1057) hydrogen bonds : angle 3.96037 ( 3141) SS BOND : bond 0.00356 ( 14) SS BOND : angle 0.51189 ( 28) covalent geometry : bond 0.00587 (17969) covalent geometry : angle 0.60495 (24258) *********************** 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 346 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 1.964 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7673 (mtp) REVERT: B 380 TYR cc_start: 0.7725 (t80) cc_final: 0.7100 (t80) REVERT: B 391 PHE cc_start: 0.6624 (m-80) cc_final: 0.6336 (m-80) REVERT: C 296 ASP cc_start: 0.8833 (t0) cc_final: 0.8558 (t0) REVERT: C 378 ASP cc_start: 0.8075 (t0) cc_final: 0.7861 (t0) REVERT: D 50 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7511 (t0) REVERT: D 243 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: F 143 ASN cc_start: 0.7995 (m-40) cc_final: 0.7001 (t0) REVERT: F 147 LYS cc_start: 0.8596 (ttmt) cc_final: 0.7447 (tppt) REVERT: F 383 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6463 (mt) REVERT: G 48 MET cc_start: 0.8404 (ptp) cc_final: 0.7898 (ppp) REVERT: G 105 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8626 (tt) outliers start: 75 outliers final: 54 residues processed: 316 average time/residue: 0.3014 time to fit residues: 141.2166 Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 262 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 40 VAL 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 B residue 361 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 50 ASP 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 261 MET 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 38 ILE 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 38 ILE 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 265 GLN Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 298 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 182 optimal weight: 0.1980 chunk 125 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 114 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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** B 309 ASN C 106 GLN C 251 HIS D 107 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.188220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133888 restraints weight = 21947.279| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.28 r_work: 0.3361 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17983 Z= 0.106 Angle : 0.483 9.315 24286 Z= 0.258 Chirality : 0.038 0.147 2647 Planarity : 0.003 0.040 2955 Dihedral : 4.043 24.519 2283 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.73 % Allowed : 17.32 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 2059 helix: 2.03 (0.15), residues: 1391 sheet: 0.20 (0.46), residues: 134 loop : -2.53 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 170 HIS 0.003 0.001 HIS G 251 PHE 0.026 0.001 PHE G 158 TYR 0.016 0.001 TYR A 279 ARG 0.003 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 1057) hydrogen bonds : angle 3.47982 ( 3141) SS BOND : bond 0.00200 ( 14) SS BOND : angle 0.42593 ( 28) covalent geometry : bond 0.00227 (17969) covalent geometry : angle 0.48343 (24258) *********************** 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 344 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 291 time to evaluate : 1.807 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7467 (mtp) REVERT: B 27 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6728 (t80) REVERT: B 380 TYR cc_start: 0.7470 (t80) cc_final: 0.6891 (t80) REVERT: C 378 ASP cc_start: 0.7833 (t0) cc_final: 0.7598 (t0) REVERT: D 243 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: D 373 MET cc_start: 0.7571 (tpp) cc_final: 0.7359 (tpt) REVERT: F 143 ASN cc_start: 0.7197 (m-40) cc_final: 0.6264 (t0) REVERT: F 147 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7273 (tppt) REVERT: G 45 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6365 (tt) REVERT: G 48 MET cc_start: 0.8181 (ptp) cc_final: 0.7711 (ppp) REVERT: G 105 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8237 (tt) REVERT: G 387 ARG cc_start: 0.4824 (mmm-85) cc_final: 0.4551 (mtp180) outliers start: 53 outliers final: 42 residues processed: 328 average time/residue: 0.2980 time to fit residues: 144.7909 Evaluate side-chains 325 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 305 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 140 LEU 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 45 LEU Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 258 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 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 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 45 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 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 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 106 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.186625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.133813 restraints weight = 22009.644| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.42 r_work: 0.3324 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2233 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= 0.130 Angle : 0.498 7.262 24286 Z= 0.266 Chirality : 0.039 0.141 2647 Planarity : 0.003 0.039 2955 Dihedral : 4.015 25.280 2283 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.99 % Allowed : 17.78 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 2059 helix: 1.98 (0.14), residues: 1398 sheet: 0.08 (0.45), residues: 136 loop : -2.53 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 170 HIS 0.004 0.001 HIS C 310 PHE 0.028 0.001 PHE G 388 TYR 0.015 0.001 TYR F 343 ARG 0.004 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1057) hydrogen bonds : angle 3.51347 ( 3141) SS BOND : bond 0.00219 ( 14) SS BOND : angle 0.41364 ( 28) covalent geometry : bond 0.00299 (17969) covalent geometry : angle 0.49761 (24258) *********************** 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 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7414 (mtp) REVERT: B 106 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: B 376 MET cc_start: 0.8330 (tpp) cc_final: 0.8126 (mmm) REVERT: B 380 TYR cc_start: 0.7489 (t80) cc_final: 0.6883 (t80) REVERT: C 378 ASP cc_start: 0.7883 (t0) cc_final: 0.7673 (t0) REVERT: D 243 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: D 373 MET cc_start: 0.7625 (tpp) cc_final: 0.7419 (tpt) REVERT: E 352 GLU cc_start: 0.7840 (tp30) cc_final: 0.7306 (tm-30) REVERT: F 49 GLN cc_start: 0.7028 (tp-100) cc_final: 0.6802 (tp40) REVERT: F 143 ASN cc_start: 0.7532 (m-40) cc_final: 0.6589 (t0) REVERT: F 248 PHE cc_start: 0.7736 (t80) cc_final: 0.7499 (t80) REVERT: F 383 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6121 (mt) REVERT: G 45 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6481 (tt) REVERT: G 48 MET cc_start: 0.8273 (ptp) cc_final: 0.7723 (ppp) REVERT: G 372 PHE cc_start: 0.6841 (t80) cc_final: 0.6469 (t80) REVERT: G 376 MET cc_start: 0.6281 (tpp) cc_final: 0.5812 (mpp) outliers start: 58 outliers final: 49 residues processed: 316 average time/residue: 0.3076 time to fit residues: 145.2585 Evaluate side-chains 327 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 140 LEU 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 37 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 258 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 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 291 VAL Chi-restraints excluded: chain F residue 126 TYR 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 45 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 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 151 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 125 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 106 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.187926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133628 restraints weight = 21870.876| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.26 r_work: 0.3362 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2333 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= 0.112 Angle : 0.485 8.360 24286 Z= 0.258 Chirality : 0.038 0.144 2647 Planarity : 0.003 0.040 2955 Dihedral : 3.954 24.924 2283 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.25 % Allowed : 17.63 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 2059 helix: 2.01 (0.14), residues: 1398 sheet: 0.23 (0.45), residues: 134 loop : -2.53 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 170 HIS 0.003 0.001 HIS C 310 PHE 0.028 0.001 PHE E 148 TYR 0.017 0.001 TYR F 343 ARG 0.004 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 1057) hydrogen bonds : angle 3.43243 ( 3141) SS BOND : bond 0.00204 ( 14) SS BOND : angle 0.39603 ( 28) covalent geometry : bond 0.00250 (17969) covalent geometry : angle 0.48507 (24258) *********************** 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 344 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7426 (mtp) REVERT: B 27 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6730 (t80) REVERT: D 243 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: E 156 GLU cc_start: 0.8317 (pt0) cc_final: 0.7909 (pp20) REVERT: F 49 GLN cc_start: 0.7068 (tp-100) cc_final: 0.6864 (tp40) REVERT: F 143 ASN cc_start: 0.7257 (m-40) cc_final: 0.6541 (t0) REVERT: F 383 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6109 (mt) REVERT: G 48 MET cc_start: 0.8241 (ptp) cc_final: 0.7720 (ppp) outliers start: 63 outliers final: 53 residues processed: 324 average time/residue: 0.3083 time to fit residues: 150.9164 Evaluate side-chains 330 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 337 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 140 LEU 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 37 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 279 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 377 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 291 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 126 TYR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 93 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 109 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 153 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 106 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.189243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134945 restraints weight = 22066.451| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.17 r_work: 0.3379 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2404 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= 0.102 Angle : 0.493 13.248 24286 Z= 0.259 Chirality : 0.038 0.147 2647 Planarity : 0.003 0.040 2955 Dihedral : 3.894 24.796 2283 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.04 % Allowed : 18.35 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 2059 helix: 2.07 (0.15), residues: 1396 sheet: 0.22 (0.44), residues: 134 loop : -2.52 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 170 HIS 0.003 0.000 HIS G 251 PHE 0.029 0.001 PHE E 148 TYR 0.017 0.001 TYR F 343 ARG 0.004 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1057) hydrogen bonds : angle 3.37303 ( 3141) SS BOND : bond 0.00170 ( 14) SS BOND : angle 0.39639 ( 28) covalent geometry : bond 0.00220 (17969) covalent geometry : angle 0.49311 (24258) *********************** 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 340 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 281 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7441 (mtp) REVERT: B 380 TYR cc_start: 0.7248 (t80) cc_final: 0.6672 (t80) REVERT: D 243 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: D 373 MET cc_start: 0.7634 (tpp) cc_final: 0.7427 (tpt) REVERT: E 156 GLU cc_start: 0.8289 (pt0) cc_final: 0.7894 (pp20) REVERT: F 49 GLN cc_start: 0.7002 (tp-100) cc_final: 0.6795 (tp-100) REVERT: F 143 ASN cc_start: 0.7232 (m-40) cc_final: 0.6534 (t0) REVERT: F 383 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6148 (mt) REVERT: G 48 MET cc_start: 0.8205 (ptp) cc_final: 0.7752 (ppp) outliers start: 59 outliers final: 50 residues processed: 320 average time/residue: 0.2913 time to fit residues: 140.0255 Evaluate side-chains 324 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 305 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 140 LEU 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 37 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 279 TYR 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 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 279 TYR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 165 CYS 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 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 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 133 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 106 GLN ** 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** G 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.186814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146174 restraints weight = 21942.401| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.44 r_work: 0.3344 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2415 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= 0.134 Angle : 0.527 12.931 24286 Z= 0.278 Chirality : 0.039 0.144 2647 Planarity : 0.003 0.040 2955 Dihedral : 3.981 25.527 2283 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.73 % Allowed : 18.81 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 2059 helix: 2.01 (0.14), residues: 1394 sheet: 0.07 (0.44), residues: 136 loop : -2.57 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 170 HIS 0.004 0.001 HIS C 310 PHE 0.032 0.001 PHE E 148 TYR 0.020 0.001 TYR F 343 ARG 0.004 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 1057) hydrogen bonds : angle 3.49383 ( 3141) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.39885 ( 28) covalent geometry : bond 0.00311 (17969) covalent geometry : angle 0.52754 (24258) ********************** 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 322 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7274 (mtm) REVERT: B 246 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7807 (ptpp) REVERT: B 380 TYR cc_start: 0.7597 (t80) cc_final: 0.6923 (t80) REVERT: D 243 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: D 373 MET cc_start: 0.7808 (tpp) cc_final: 0.7582 (tpt) REVERT: E 156 GLU cc_start: 0.8249 (pt0) cc_final: 0.7831 (pp20) REVERT: F 143 ASN cc_start: 0.7613 (m-40) cc_final: 0.6667 (t0) REVERT: F 383 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6293 (mt) REVERT: G 48 MET cc_start: 0.8291 (ptp) cc_final: 0.7834 (ppp) outliers start: 53 outliers final: 46 residues processed: 305 average time/residue: 0.3728 time to fit residues: 170.5113 Evaluate side-chains 315 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 305 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 45 LEU 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 37 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 338 LEU 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 279 TYR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 165 CYS 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 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 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 8 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 106 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.186488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145728 restraints weight = 21910.137| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.35 r_work: 0.3333 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2437 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= 0.136 Angle : 0.536 16.647 24286 Z= 0.281 Chirality : 0.039 0.162 2647 Planarity : 0.003 0.041 2955 Dihedral : 4.018 25.231 2283 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.14 % Allowed : 18.56 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 2059 helix: 1.99 (0.14), residues: 1395 sheet: 0.05 (0.44), residues: 136 loop : -2.58 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 170 HIS 0.003 0.001 HIS C 310 PHE 0.031 0.001 PHE E 148 TYR 0.020 0.001 TYR F 343 ARG 0.005 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 1057) hydrogen bonds : angle 3.51754 ( 3141) SS BOND : bond 0.00232 ( 14) SS BOND : angle 0.39208 ( 28) covalent geometry : bond 0.00315 (17969) covalent geometry : angle 0.53616 (24258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11270.86 seconds wall clock time: 196 minutes 39.37 seconds (11799.37 seconds total)