Starting phenix.real_space_refine on Sat Aug 23 14:18:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l99_62898/08_2025/9l99_62898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l99_62898/08_2025/9l99_62898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l99_62898/08_2025/9l99_62898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l99_62898/08_2025/9l99_62898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l99_62898/08_2025/9l99_62898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l99_62898/08_2025/9l99_62898.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 83 5.16 5 C 8038 2.51 5 N 2182 2.21 5 O 2405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12710 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3122 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 27, 'TRANS': 383} Chain: "B" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2929 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 25, 'TRANS': 343} Chain: "G" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3122 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 27, 'TRANS': 383} Chain: "H" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2929 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 25, 'TRANS': 343} Chain: "N" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.46, per 1000 atoms: 0.27 Number of scatterers: 12710 At special positions: 0 Unit cell: (155.44, 144.72, 143.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 83 16.00 O 2405 8.00 N 2182 7.00 C 8038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.04 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 25 " distance=2.03 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 226 " distance=2.02 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 45 " distance=2.04 Simple disulfide: pdb=" SG CYS N 40 " - pdb=" SG CYS N 58 " distance=2.04 Simple disulfide: pdb=" SG CYS N 52 " - pdb=" SG CYS N 67 " distance=2.03 Simple disulfide: pdb=" SG CYS N 72 " - pdb=" SG CYS N 84 " distance=2.03 Simple disulfide: pdb=" SG CYS N 79 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 108 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 469.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 41 sheets defined 6.3% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.515A pdb=" N ASN A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.758A pdb=" N GLU A 253 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 254' Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.041A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'B' and resid 5 through 9 removed outlier: 4.124A pdb=" N LEU B 8 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 9 " --> pdb=" O PHE B 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5 through 9' Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 352 through 362 removed outlier: 3.751A pdb=" N ILE B 356 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 357 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 254 removed outlier: 3.517A pdb=" N THR G 254 " --> pdb=" O LEU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.162A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 411 Processing helix chain 'H' and resid 79 through 81 No H-bonds generated for 'chain 'H' and resid 79 through 81' Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 222 through 226 removed outlier: 4.022A pdb=" N CYS H 226 " --> pdb=" O ALA H 223 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.821A pdb=" N ILE A 280 " --> pdb=" O HIS A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 5.882A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 144 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 48 removed outlier: 5.571A pdb=" N LYS A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 123 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.843A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 79 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 removed outlier: 3.507A pdb=" N ARG A 220 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 302 removed outlier: 5.682A pdb=" N GLU A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 321 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 338 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.702A pdb=" N GLY A 326 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 365 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 376 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB2, first strand: chain 'B' and resid 31 through 35 removed outlier: 7.673A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR B 99 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N ALA B 49 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS B 97 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N PHE B 51 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N GLY B 95 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 63 through 65 Processing sheet with id=AB4, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.656A pdb=" N VAL B 113 " --> pdb=" O CYS B 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 148 through 155 Processing sheet with id=AB6, first strand: chain 'B' and resid 237 through 238 removed outlier: 3.529A pdb=" N LEU B 255 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 253 " --> pdb=" O MET B 168 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.774A pdb=" N TYR B 188 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 206 through 211 removed outlier: 3.631A pdb=" N VAL B 197 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 229 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 227 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 275 through 279 removed outlier: 4.350A pdb=" N THR B 275 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP B 279 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 285 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 317 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 307 through 311 removed outlier: 3.620A pdb=" N THR B 297 " --> pdb=" O THR B 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.950A pdb=" N LYS G 160 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.817A pdb=" N VAL G 19 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 30 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLY G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER G 36 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS G 130 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR G 137 " --> pdb=" O THR G 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 46 through 48 removed outlier: 4.258A pdb=" N TYR G 46 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL G 177 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL G 178 " --> pdb=" O TYR G 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.734A pdb=" N GLU G 109 " --> pdb=" O HIS G 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.734A pdb=" N GLU G 109 " --> pdb=" O HIS G 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR G 77 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AC8, first strand: chain 'G' and resid 220 through 221 removed outlier: 3.510A pdb=" N ARG G 220 " --> pdb=" O THR G 234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 234 " --> pdb=" O ARG G 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 296 through 303 removed outlier: 4.991A pdb=" N GLU G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS G 321 " --> pdb=" O GLU G 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 306 through 307 removed outlier: 7.269A pdb=" N CYS G 306 " --> pdb=" O LYS G 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 343 through 346 removed outlier: 3.531A pdb=" N THR G 344 " --> pdb=" O CYS G 328 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS G 331 " --> pdb=" O SER G 368 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 369 " --> pdb=" O LYS G 372 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 387 through 388 removed outlier: 3.644A pdb=" N VAL H 336 " --> pdb=" O TYR H 328 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR H 296 " --> pdb=" O VAL H 329 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 14 through 16 Processing sheet with id=AD5, first strand: chain 'H' and resid 31 through 35 removed outlier: 6.923A pdb=" N GLN H 46 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL H 34 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG H 44 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N TYR H 99 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ALA H 49 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS H 97 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N PHE H 51 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N GLY H 95 " --> pdb=" O PHE H 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 66 through 67 removed outlier: 3.877A pdb=" N TYR H 66 " --> pdb=" O LYS H 76 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 83 through 86 Processing sheet with id=AD8, first strand: chain 'H' and resid 148 through 155 removed outlier: 3.537A pdb=" N LYS H 148 " --> pdb=" O VAL H 268 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 237 through 238 Processing sheet with id=AE1, first strand: chain 'H' and resid 180 through 182 Processing sheet with id=AE2, first strand: chain 'H' and resid 207 through 211 removed outlier: 3.635A pdb=" N GLU H 200 " --> pdb=" O ILE H 227 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE H 227 " --> pdb=" O GLU H 200 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 275 through 279 removed outlier: 3.784A pdb=" N THR H 275 " --> pdb=" O HIS H 286 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR H 277 " --> pdb=" O THR H 284 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR H 284 " --> pdb=" O THR H 277 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP H 279 " --> pdb=" O GLY H 282 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 37 through 39 Processing sheet with id=AE5, first strand: chain 'N' and resid 76 through 78 276 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4124 1.35 - 1.48: 3366 1.48 - 1.61: 5466 1.61 - 1.74: 0 1.74 - 1.86: 98 Bond restraints: 13054 Sorted by residual: bond pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CA CYS H 226 " pdb=" CB CYS H 226 " ideal model delta sigma weight residual 1.533 1.507 0.026 1.65e-02 3.67e+03 2.52e+00 bond pdb=" CB GLU G 298 " pdb=" CG GLU G 298 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CB ASN A 139 " pdb=" CG ASN A 139 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.13e+00 bond pdb=" CG PRO A 265 " pdb=" CD PRO A 265 " ideal model delta sigma weight residual 1.503 1.454 0.049 3.40e-02 8.65e+02 2.06e+00 ... (remaining 13049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 17461 2.17 - 4.34: 282 4.34 - 6.51: 26 6.51 - 8.68: 7 8.68 - 10.85: 2 Bond angle restraints: 17778 Sorted by residual: angle pdb=" CA CYS H 226 " pdb=" CB CYS H 226 " pdb=" SG CYS H 226 " ideal model delta sigma weight residual 114.40 125.25 -10.85 2.30e+00 1.89e-01 2.23e+01 angle pdb=" N VAL A 148 " pdb=" CA VAL A 148 " pdb=" C VAL A 148 " ideal model delta sigma weight residual 112.90 108.79 4.11 9.60e-01 1.09e+00 1.83e+01 angle pdb=" CA GLN A 93 " pdb=" C GLN A 93 " pdb=" N CYS A 94 " ideal model delta sigma weight residual 118.43 123.71 -5.28 1.33e+00 5.65e-01 1.58e+01 angle pdb=" CA CYS H 201 " pdb=" CB CYS H 201 " pdb=" SG CYS H 201 " ideal model delta sigma weight residual 114.40 123.26 -8.86 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CA LYS B 202 " pdb=" CB LYS B 202 " pdb=" CG LYS B 202 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 ... (remaining 17773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 7109 18.01 - 36.02: 604 36.02 - 54.02: 121 54.02 - 72.03: 22 72.03 - 90.04: 12 Dihedral angle restraints: 7868 sinusoidal: 3109 harmonic: 4759 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 124 " pdb=" CB CYS B 124 " ideal model delta sinusoidal sigma weight residual 93.00 -177.71 -89.29 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS N 79 " pdb=" SG CYS N 79 " pdb=" SG CYS N 97 " pdb=" CB CYS N 97 " ideal model delta sinusoidal sigma weight residual 93.00 172.56 -79.56 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS H 203 " pdb=" SG CYS H 203 " pdb=" SG CYS H 220 " pdb=" CB CYS H 220 " ideal model delta sinusoidal sigma weight residual -86.00 -161.31 75.31 1 1.00e+01 1.00e-02 7.17e+01 ... (remaining 7865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1338 0.039 - 0.077: 429 0.077 - 0.116: 165 0.116 - 0.155: 37 0.155 - 0.193: 5 Chirality restraints: 1974 Sorted by residual: chirality pdb=" CG LEU G 18 " pdb=" CB LEU G 18 " pdb=" CD1 LEU G 18 " pdb=" CD2 LEU G 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA CYS H 226 " pdb=" N CYS H 226 " pdb=" C CYS H 226 " pdb=" CB CYS H 226 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CB THR G 126 " pdb=" CA THR G 126 " pdb=" OG1 THR G 126 " pdb=" CG2 THR G 126 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 1971 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 264 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 265 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 298 " -0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CD GLU G 298 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU G 298 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU G 298 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 298 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C GLU G 298 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU G 298 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL G 299 " -0.014 2.00e-02 2.50e+03 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 532 2.71 - 3.26: 11844 3.26 - 3.81: 18720 3.81 - 4.35: 22128 4.35 - 4.90: 39722 Nonbonded interactions: 92946 Sorted by model distance: nonbonded pdb=" O TRP N 89 " pdb="CA CA N 202 " model vdw 2.164 2.510 nonbonded pdb=" O ASP G 385 " pdb=" NE2 GLN H 341 " model vdw 2.212 3.120 nonbonded pdb=" O PHE B 26 " pdb=" OH TYR B 69 " model vdw 2.218 3.040 nonbonded pdb=" OG SER G 309 " pdb=" OE1 GLN H 341 " model vdw 2.232 3.040 nonbonded pdb=" O ASP A 385 " pdb=" NE2 GLN B 341 " model vdw 2.246 3.120 ... (remaining 92941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 0.055 13088 Z= 0.152 Angle : 0.681 10.852 17846 Z= 0.379 Chirality : 0.045 0.193 1974 Planarity : 0.005 0.107 2288 Dihedral : 13.546 90.041 4710 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.14 % Allowed : 17.02 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.20), residues: 1630 helix: -1.29 (0.60), residues: 74 sheet: -1.84 (0.21), residues: 536 loop : -1.91 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.014 0.001 TYR A 308 PHE 0.021 0.001 PHE G 95 TRP 0.010 0.001 TRP B 279 HIS 0.005 0.001 HIS H 169 Details of bonding type rmsd covalent geometry : bond 0.00333 (13054) covalent geometry : angle 0.66756 (17778) SS BOND : bond 0.00358 ( 34) SS BOND : angle 2.31329 ( 68) hydrogen bonds : bond 0.28358 ( 274) hydrogen bonds : angle 10.35360 ( 687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.288 Fit side-chains REVERT: A 145 ASP cc_start: 0.7933 (p0) cc_final: 0.7545 (p0) REVERT: B 69 TYR cc_start: 0.7475 (m-80) cc_final: 0.6835 (m-80) REVERT: N 37 GLN cc_start: 0.7583 (mt0) cc_final: 0.7246 (pt0) outliers start: 2 outliers final: 2 residues processed: 163 average time/residue: 0.0812 time to fit residues: 19.8732 Evaluate side-chains 153 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 18 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 149 ASN A 230 HIS A 333 HIS A 392 HIS B 96 HIS B 153 HIS B 174 HIS B 214 GLN B 246 HIS G 43 ASN G 246 ASN G 275 HIS G 364 ASN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.142322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.103205 restraints weight = 15697.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.104352 restraints weight = 12668.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.104306 restraints weight = 12677.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.105054 restraints weight = 9176.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.105204 restraints weight = 7953.622| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13088 Z= 0.234 Angle : 0.706 8.957 17846 Z= 0.369 Chirality : 0.050 0.182 1974 Planarity : 0.005 0.077 2288 Dihedral : 5.892 58.436 1771 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 5.74 % Allowed : 13.19 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.20), residues: 1630 helix: -1.21 (0.61), residues: 72 sheet: -1.79 (0.21), residues: 552 loop : -1.90 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 180 TYR 0.019 0.002 TYR H 165 PHE 0.019 0.002 PHE H 238 TRP 0.010 0.001 TRP B 279 HIS 0.009 0.002 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00588 (13054) covalent geometry : angle 0.69478 (17778) SS BOND : bond 0.00399 ( 34) SS BOND : angle 2.10579 ( 68) hydrogen bonds : bond 0.04578 ( 274) hydrogen bonds : angle 7.10526 ( 687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 0.360 Fit side-chains REVERT: A 407 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.6259 (m-10) REVERT: B 37 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7568 (mt-10) REVERT: B 67 MET cc_start: 0.8178 (tpp) cc_final: 0.7915 (tpp) REVERT: B 199 TYR cc_start: 0.8280 (p90) cc_final: 0.7953 (p90) REVERT: G 43 ASN cc_start: 0.8545 (t0) cc_final: 0.8177 (t0) REVERT: G 230 HIS cc_start: 0.8975 (OUTLIER) cc_final: 0.8557 (p-80) REVERT: H 197 VAL cc_start: 0.8469 (m) cc_final: 0.8260 (m) outliers start: 81 outliers final: 54 residues processed: 230 average time/residue: 0.0757 time to fit residues: 26.6893 Evaluate side-chains 207 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 364 ASN Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 85 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS G 125 HIS G 246 ASN G 275 HIS G 364 ASN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.144168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109323 restraints weight = 15773.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.107271 restraints weight = 18859.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.108573 restraints weight = 19505.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.108896 restraints weight = 13086.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109414 restraints weight = 13067.383| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13088 Z= 0.172 Angle : 0.641 8.013 17846 Z= 0.335 Chirality : 0.047 0.178 1974 Planarity : 0.005 0.056 2288 Dihedral : 5.702 58.953 1771 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.32 % Allowed : 14.89 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.20), residues: 1630 helix: -1.14 (0.61), residues: 72 sheet: -1.56 (0.22), residues: 546 loop : -1.82 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 20 TYR 0.019 0.002 TYR H 165 PHE 0.014 0.001 PHE A 51 TRP 0.008 0.001 TRP B 279 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00432 (13054) covalent geometry : angle 0.63187 (17778) SS BOND : bond 0.00330 ( 34) SS BOND : angle 1.87499 ( 68) hydrogen bonds : bond 0.03816 ( 274) hydrogen bonds : angle 6.58695 ( 687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 159 time to evaluate : 0.354 Fit side-chains REVERT: A 231 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8695 (p) REVERT: A 407 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.6447 (m-10) REVERT: B 67 MET cc_start: 0.8152 (tpp) cc_final: 0.7847 (tpp) REVERT: B 195 LYS cc_start: 0.7539 (mmmt) cc_final: 0.7317 (mmmt) REVERT: B 199 TYR cc_start: 0.8302 (p90) cc_final: 0.8027 (p90) REVERT: G 43 ASN cc_start: 0.8572 (t0) cc_final: 0.8170 (t0) REVERT: G 109 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7344 (pt0) REVERT: H 197 VAL cc_start: 0.8451 (m) cc_final: 0.8234 (m) outliers start: 75 outliers final: 51 residues processed: 217 average time/residue: 0.0729 time to fit residues: 24.8524 Evaluate side-chains 203 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 33 ASN G 246 ASN G 275 HIS G 364 ASN H 71 HIS ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.141619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.106735 restraints weight = 15857.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104873 restraints weight = 19433.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.105976 restraints weight = 20182.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.106650 restraints weight = 13524.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.107040 restraints weight = 12200.211| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13088 Z= 0.225 Angle : 0.683 8.219 17846 Z= 0.355 Chirality : 0.049 0.213 1974 Planarity : 0.005 0.056 2288 Dihedral : 5.802 57.551 1771 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 7.23 % Allowed : 14.82 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.20), residues: 1630 helix: -1.25 (0.59), residues: 72 sheet: -1.49 (0.22), residues: 546 loop : -1.86 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 267 TYR 0.020 0.002 TYR H 165 PHE 0.019 0.002 PHE H 238 TRP 0.009 0.001 TRP B 279 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00568 (13054) covalent geometry : angle 0.67342 (17778) SS BOND : bond 0.00356 ( 34) SS BOND : angle 1.99891 ( 68) hydrogen bonds : bond 0.03863 ( 274) hydrogen bonds : angle 6.38746 ( 687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 163 time to evaluate : 0.447 Fit side-chains REVERT: A 204 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: A 252 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: A 407 TRP cc_start: 0.7111 (OUTLIER) cc_final: 0.6467 (m-10) REVERT: B 8 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9066 (pp) REVERT: B 18 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: B 195 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7356 (mmmt) REVERT: B 199 TYR cc_start: 0.8439 (p90) cc_final: 0.7956 (p90) REVERT: G 15 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6192 (p90) REVERT: G 43 ASN cc_start: 0.8591 (t0) cc_final: 0.8120 (t0) REVERT: H 197 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8220 (m) REVERT: H 217 MET cc_start: 0.6280 (mtp) cc_final: 0.6027 (mtp) outliers start: 102 outliers final: 71 residues processed: 245 average time/residue: 0.0774 time to fit residues: 29.7843 Evaluate side-chains 233 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 155 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 364 ASN Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 102 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 ASN ** H 169 HIS ** 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 = 0.3496 r_free = 0.3496 target = 0.143997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.109761 restraints weight = 15877.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.107022 restraints weight = 23953.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108757 restraints weight = 23064.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.108976 restraints weight = 14444.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.109309 restraints weight = 13315.704| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13088 Z= 0.145 Angle : 0.608 7.501 17846 Z= 0.317 Chirality : 0.046 0.174 1974 Planarity : 0.004 0.048 2288 Dihedral : 5.369 56.930 1769 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 7.02 % Allowed : 15.89 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.20), residues: 1630 helix: -1.13 (0.61), residues: 72 sheet: -1.31 (0.22), residues: 532 loop : -1.73 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.017 0.001 TYR H 165 PHE 0.013 0.001 PHE A 51 TRP 0.008 0.001 TRP B 279 HIS 0.014 0.001 HIS G 331 Details of bonding type rmsd covalent geometry : bond 0.00363 (13054) covalent geometry : angle 0.59981 (17778) SS BOND : bond 0.00301 ( 34) SS BOND : angle 1.73711 ( 68) hydrogen bonds : bond 0.03275 ( 274) hydrogen bonds : angle 6.06616 ( 687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 168 time to evaluate : 0.471 Fit side-chains REVERT: A 407 TRP cc_start: 0.7114 (OUTLIER) cc_final: 0.6475 (m-10) REVERT: B 8 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9023 (pp) REVERT: B 195 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7364 (mmmt) REVERT: B 199 TYR cc_start: 0.8416 (p90) cc_final: 0.7955 (p90) REVERT: G 43 ASN cc_start: 0.8592 (t0) cc_final: 0.8174 (t0) REVERT: G 109 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: G 252 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8079 (mm110) REVERT: H 197 VAL cc_start: 0.8343 (m) cc_final: 0.8140 (m) outliers start: 99 outliers final: 70 residues processed: 252 average time/residue: 0.0818 time to fit residues: 31.6481 Evaluate side-chains 229 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 155 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.0070 chunk 139 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 ASN G 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.142326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.107133 restraints weight = 15816.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.105165 restraints weight = 19899.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.106897 restraints weight = 19324.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106952 restraints weight = 12252.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.107264 restraints weight = 11884.523| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13088 Z= 0.196 Angle : 0.652 8.141 17846 Z= 0.338 Chirality : 0.048 0.226 1974 Planarity : 0.005 0.052 2288 Dihedral : 5.469 55.459 1769 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 8.01 % Allowed : 14.68 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.20), residues: 1630 helix: -1.19 (0.60), residues: 72 sheet: -1.34 (0.22), residues: 546 loop : -1.75 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.021 0.002 TYR H 165 PHE 0.015 0.001 PHE A 51 TRP 0.008 0.001 TRP B 279 HIS 0.011 0.001 HIS G 331 Details of bonding type rmsd covalent geometry : bond 0.00498 (13054) covalent geometry : angle 0.64309 (17778) SS BOND : bond 0.00347 ( 34) SS BOND : angle 1.89009 ( 68) hydrogen bonds : bond 0.03487 ( 274) hydrogen bonds : angle 6.03321 ( 687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 162 time to evaluate : 0.359 Fit side-chains REVERT: A 252 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: A 407 TRP cc_start: 0.7057 (OUTLIER) cc_final: 0.6294 (m-10) REVERT: B 8 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9026 (pp) REVERT: B 18 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: B 195 LYS cc_start: 0.7604 (mmmt) cc_final: 0.7325 (mmmt) REVERT: B 199 TYR cc_start: 0.8432 (p90) cc_final: 0.8002 (p90) REVERT: G 15 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6058 (p90) REVERT: G 220 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.9008 (ptp-110) REVERT: G 252 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8103 (mm110) REVERT: G 298 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6318 (tm-30) REVERT: H 197 VAL cc_start: 0.8374 (m) cc_final: 0.8139 (m) REVERT: N 89 TRP cc_start: 0.6183 (m-10) cc_final: 0.5895 (m-10) outliers start: 113 outliers final: 90 residues processed: 257 average time/residue: 0.0773 time to fit residues: 30.8408 Evaluate side-chains 255 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 158 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 364 ASN Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 260 ARG Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 133 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.143394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.110016 restraints weight = 15729.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108859 restraints weight = 20969.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.110012 restraints weight = 19744.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.110031 restraints weight = 14164.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.110273 restraints weight = 15425.293| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13088 Z= 0.161 Angle : 0.623 8.501 17846 Z= 0.322 Chirality : 0.047 0.177 1974 Planarity : 0.004 0.046 2288 Dihedral : 5.319 54.404 1769 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 7.87 % Allowed : 16.03 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.20), residues: 1630 helix: -1.14 (0.61), residues: 72 sheet: -1.23 (0.22), residues: 544 loop : -1.70 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.021 0.002 TYR A 46 PHE 0.013 0.001 PHE A 51 TRP 0.008 0.001 TRP B 279 HIS 0.014 0.001 HIS G 331 Details of bonding type rmsd covalent geometry : bond 0.00405 (13054) covalent geometry : angle 0.61433 (17778) SS BOND : bond 0.00311 ( 34) SS BOND : angle 1.74181 ( 68) hydrogen bonds : bond 0.03247 ( 274) hydrogen bonds : angle 5.88797 ( 687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 164 time to evaluate : 0.463 Fit side-chains REVERT: A 204 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: A 252 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: A 407 TRP cc_start: 0.7052 (OUTLIER) cc_final: 0.6435 (m-10) REVERT: B 18 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: B 195 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7364 (mmmt) REVERT: B 199 TYR cc_start: 0.8393 (p90) cc_final: 0.7999 (p90) REVERT: G 15 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.5678 (p90) REVERT: G 43 ASN cc_start: 0.8536 (t0) cc_final: 0.8290 (t0) REVERT: G 109 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: G 220 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.9018 (ptp-110) REVERT: G 252 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7859 (mm110) REVERT: G 298 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6281 (tm-30) REVERT: H 197 VAL cc_start: 0.8330 (m) cc_final: 0.8099 (m) REVERT: N 89 TRP cc_start: 0.6187 (m-10) cc_final: 0.5896 (m-10) outliers start: 111 outliers final: 90 residues processed: 257 average time/residue: 0.0803 time to fit residues: 31.7128 Evaluate side-chains 253 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 155 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 260 ARG Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 15 optimal weight: 0.0870 chunk 128 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.0050 chunk 88 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN ** G 331 HIS ** 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 = 0.3509 r_free = 0.3509 target = 0.145177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110428 restraints weight = 15610.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.109004 restraints weight = 20443.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.110110 restraints weight = 21667.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.110304 restraints weight = 12587.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.110747 restraints weight = 11216.859| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13088 Z= 0.117 Angle : 0.587 8.623 17846 Z= 0.304 Chirality : 0.046 0.262 1974 Planarity : 0.004 0.046 2288 Dihedral : 5.085 54.076 1769 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.45 % Allowed : 17.66 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.21), residues: 1630 helix: -1.05 (0.62), residues: 72 sheet: -1.11 (0.23), residues: 532 loop : -1.58 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.020 0.001 TYR A 15 PHE 0.010 0.001 PHE H 64 TRP 0.008 0.001 TRP A 243 HIS 0.012 0.001 HIS G 331 Details of bonding type rmsd covalent geometry : bond 0.00288 (13054) covalent geometry : angle 0.58008 (17778) SS BOND : bond 0.00265 ( 34) SS BOND : angle 1.54898 ( 68) hydrogen bonds : bond 0.02922 ( 274) hydrogen bonds : angle 5.70428 ( 687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 168 time to evaluate : 0.298 Fit side-chains REVERT: A 69 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7964 (pttp) REVERT: A 204 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8374 (mt0) REVERT: A 407 TRP cc_start: 0.6919 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: B 18 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: B 195 LYS cc_start: 0.7591 (mmmt) cc_final: 0.7297 (mmmt) REVERT: B 199 TYR cc_start: 0.8463 (p90) cc_final: 0.8084 (p90) REVERT: G 43 ASN cc_start: 0.8554 (t0) cc_final: 0.8337 (t0) REVERT: G 102 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: G 109 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7190 (pt0) REVERT: G 220 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8997 (ptp-110) REVERT: G 252 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7814 (mm110) REVERT: G 298 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6302 (tm-30) REVERT: G 372 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7511 (mmmt) REVERT: H 112 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8779 (p) REVERT: H 187 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7776 (p) REVERT: H 197 VAL cc_start: 0.8308 (m) cc_final: 0.8104 (m) REVERT: N 89 TRP cc_start: 0.6144 (m-10) cc_final: 0.5867 (m-10) outliers start: 91 outliers final: 67 residues processed: 246 average time/residue: 0.0779 time to fit residues: 29.1505 Evaluate side-chains 232 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 154 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 148 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN ** H 239 ASN ** 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 = 0.3515 r_free = 0.3515 target = 0.145835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.111049 restraints weight = 15679.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109383 restraints weight = 19936.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110689 restraints weight = 21572.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.110985 restraints weight = 12149.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.111458 restraints weight = 10607.458| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13088 Z= 0.115 Angle : 0.579 8.479 17846 Z= 0.299 Chirality : 0.045 0.170 1974 Planarity : 0.005 0.104 2288 Dihedral : 4.945 53.927 1769 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 5.96 % Allowed : 18.01 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.21), residues: 1630 helix: -1.04 (0.62), residues: 72 sheet: -0.97 (0.23), residues: 526 loop : -1.53 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.021 0.001 TYR A 15 PHE 0.010 0.001 PHE H 64 TRP 0.008 0.001 TRP B 279 HIS 0.011 0.001 HIS G 331 Details of bonding type rmsd covalent geometry : bond 0.00284 (13054) covalent geometry : angle 0.57233 (17778) SS BOND : bond 0.00267 ( 34) SS BOND : angle 1.49076 ( 68) hydrogen bonds : bond 0.02806 ( 274) hydrogen bonds : angle 5.54571 ( 687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 160 time to evaluate : 0.393 Fit side-chains REVERT: A 69 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7929 (pttp) REVERT: A 204 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8414 (mt0) REVERT: A 252 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: A 407 TRP cc_start: 0.6950 (OUTLIER) cc_final: 0.6278 (m-10) REVERT: B 18 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: B 195 LYS cc_start: 0.7594 (mmmt) cc_final: 0.7313 (mmmt) REVERT: G 102 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8725 (tt0) REVERT: G 109 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7177 (pt0) REVERT: G 220 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8998 (ptp-110) REVERT: G 242 MET cc_start: 0.7464 (tpt) cc_final: 0.7185 (tpt) REVERT: G 252 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7798 (mm110) REVERT: G 298 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6367 (tm-30) REVERT: G 372 LYS cc_start: 0.7883 (mmtm) cc_final: 0.7534 (mmmt) REVERT: H 112 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8780 (p) REVERT: H 187 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7766 (p) REVERT: N 89 TRP cc_start: 0.6113 (m-10) cc_final: 0.5856 (m-10) outliers start: 84 outliers final: 67 residues processed: 230 average time/residue: 0.0817 time to fit residues: 28.9196 Evaluate side-chains 228 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 151 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 ASN G 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.143717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109378 restraints weight = 15834.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.107361 restraints weight = 20049.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.108622 restraints weight = 20012.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.109178 restraints weight = 13259.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109655 restraints weight = 12387.324| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13088 Z= 0.164 Angle : 0.622 8.721 17846 Z= 0.320 Chirality : 0.047 0.252 1974 Planarity : 0.005 0.098 2288 Dihedral : 5.123 53.467 1769 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 6.24 % Allowed : 17.80 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.21), residues: 1630 helix: -1.04 (0.61), residues: 72 sheet: -1.00 (0.23), residues: 542 loop : -1.60 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 298 TYR 0.021 0.001 TYR A 15 PHE 0.013 0.001 PHE A 51 TRP 0.007 0.001 TRP G 89 HIS 0.011 0.001 HIS G 331 Details of bonding type rmsd covalent geometry : bond 0.00415 (13054) covalent geometry : angle 0.61459 (17778) SS BOND : bond 0.00306 ( 34) SS BOND : angle 1.65173 ( 68) hydrogen bonds : bond 0.03144 ( 274) hydrogen bonds : angle 5.64119 ( 687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 154 time to evaluate : 0.470 Fit side-chains REVERT: A 69 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7898 (pttp) REVERT: A 204 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: A 252 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: A 407 TRP cc_start: 0.7159 (OUTLIER) cc_final: 0.6439 (m-10) REVERT: B 18 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: B 195 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7344 (mmmt) REVERT: G 109 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: G 220 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8992 (ptp-110) REVERT: G 242 MET cc_start: 0.7458 (tpt) cc_final: 0.7182 (tpt) REVERT: G 252 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7917 (mm110) REVERT: G 298 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6459 (tm-30) REVERT: G 372 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7579 (mmmt) REVERT: G 381 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7243 (mptt) REVERT: H 187 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7786 (p) REVERT: N 89 TRP cc_start: 0.6120 (m-10) cc_final: 0.5811 (m-10) outliers start: 88 outliers final: 78 residues processed: 226 average time/residue: 0.0971 time to fit residues: 33.4305 Evaluate side-chains 238 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 152 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 364 ASN Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 159 optimal weight: 0.4980 chunk 17 optimal weight: 0.0010 chunk 60 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN H 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.145971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.110989 restraints weight = 15683.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.109248 restraints weight = 19221.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.111000 restraints weight = 19179.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.110959 restraints weight = 12007.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.111355 restraints weight = 11846.021| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13088 Z= 0.111 Angle : 0.581 8.933 17846 Z= 0.299 Chirality : 0.045 0.170 1974 Planarity : 0.004 0.092 2288 Dihedral : 4.945 53.472 1769 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.96 % Allowed : 18.37 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.21), residues: 1630 helix: -1.04 (0.62), residues: 72 sheet: -0.90 (0.23), residues: 526 loop : -1.49 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.021 0.001 TYR A 15 PHE 0.010 0.001 PHE H 64 TRP 0.009 0.001 TRP A 243 HIS 0.011 0.001 HIS G 331 Details of bonding type rmsd covalent geometry : bond 0.00269 (13054) covalent geometry : angle 0.57434 (17778) SS BOND : bond 0.00262 ( 34) SS BOND : angle 1.48610 ( 68) hydrogen bonds : bond 0.02804 ( 274) hydrogen bonds : angle 5.49019 ( 687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.54 seconds wall clock time: 32 minutes 40.45 seconds (1960.45 seconds total)