Starting phenix.real_space_refine on Fri Jul 3 06:33:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l99_62898/07_2026/9l99_62898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l99_62898/07_2026/9l99_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9l99_62898/07_2026/9l99_62898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l99_62898/07_2026/9l99_62898.map" model { file = "/net/cci-nas-00/data/ceres_data/9l99_62898/07_2026/9l99_62898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l99_62898/07_2026/9l99_62898.cif" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 3.13, per 1000 atoms: 0.25 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: 0.97 Conformation dependent library (CDL) restraints added in 770.8 milliseconds 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: 0.44 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: 2.04 Time building geometry restraints manager: 1.49 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 3.250 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: 0.660 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.320 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 are 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/Z covalent geometry : bond 0.00333 / 0.15 (13054) covalent geometry : angle 0.66756 / 0.37 (17778) SS BOND : bond 0.00358 / 0.24 ( 34) SS BOND : angle 2.31329 / 1.64 ( 68) hydrogen bonds : bond 0.28358 / 19.24 ( 274) hydrogen bonds : angle 10.35360 / 7.04 ( 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 : 0.504 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: 0.1033 time to fit residues: 25.5471 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 : 0.521 ------------------------------------------------------------------------------- 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... A 125 HIS A 149 ASN A 230 HIS A 333 HIS A 392 HIS B 96 HIS B 153 HIS ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** H 252 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.141877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.104864 restraints weight = 15681.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.102987 restraints weight = 13542.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.104505 restraints weight = 14732.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.104639 restraints weight = 10999.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.105482 restraints weight = 11044.285| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13088 Z= 0.234 Angle : 0.712 8.903 17846 Z= 0.372 Chirality : 0.050 0.184 1974 Planarity : 0.005 0.076 2288 Dihedral : 5.963 59.217 1771 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 5.96 % Allowed : 13.55 % Favored : 80.50 % 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 are not related in a simple way. whole: -2.74 (0.20), residues: 1630 helix: -1.22 (0.61), residues: 72 sheet: -1.80 (0.21), residues: 552 loop : -1.91 (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 A 51 TRP 0.011 0.001 TRP B 279 HIS 0.009 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.23 (13054) covalent geometry : angle 0.70128 / 0.37 (17778) SS BOND : bond 0.00404 / 0.26 ( 34) SS BOND : angle 2.10463 / 1.47 ( 68) hydrogen bonds : bond 0.04485 / 2.94 ( 274) hydrogen bonds : angle 7.00083 / 4.78 ( 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 249 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 165 time to evaluate : 0.415 Fit side-chains REVERT: A 407 TRP cc_start: 0.6791 (OUTLIER) cc_final: 0.6223 (m-10) REVERT: B 37 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7548 (mt-10) REVERT: B 67 MET cc_start: 0.8217 (tpp) cc_final: 0.7956 (tpp) REVERT: B 199 TYR cc_start: 0.8279 (p90) cc_final: 0.7961 (p90) REVERT: G 43 ASN cc_start: 0.8568 (t0) cc_final: 0.8203 (t0) REVERT: G 230 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8581 (p-80) outliers start: 84 outliers final: 57 residues processed: 235 average time/residue: 0.0919 time to fit residues: 33.0466 Evaluate side-chains 209 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 129 LEU 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 87 THR 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 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: 0.8980 chunk 109 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 141 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 HIS ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN G 125 HIS G 246 ASN G 275 HIS G 364 ASN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.145848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109421 restraints weight = 15896.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107337 restraints weight = 14303.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.109000 restraints weight = 15243.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.108928 restraints weight = 10875.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.109066 restraints weight = 11933.051| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1313 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= 0.120 Angle : 0.595 7.492 17846 Z= 0.312 Chirality : 0.045 0.174 1974 Planarity : 0.004 0.051 2288 Dihedral : 5.493 58.506 1771 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.75 % Allowed : 15.74 % Favored : 79.50 % 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 are not related in a simple way. whole: -2.40 (0.20), residues: 1630 helix: -1.07 (0.63), residues: 72 sheet: -1.50 (0.22), residues: 536 loop : -1.72 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 20 TYR 0.016 0.001 TYR H 165 PHE 0.010 0.001 PHE A 51 TRP 0.007 0.001 TRP B 279 HIS 0.008 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (13054) covalent geometry : angle 0.58702 / 0.31 (17778) SS BOND : bond 0.00311 / 0.20 ( 34) SS BOND : angle 1.69541 / 1.16 ( 68) hydrogen bonds : bond 0.03473 / 2.25 ( 274) hydrogen bonds : angle 6.38353 / 4.35 ( 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 235 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 168 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 231 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 407 TRP cc_start: 0.6893 (OUTLIER) cc_final: 0.6360 (m-10) REVERT: B 67 MET cc_start: 0.8090 (tpp) cc_final: 0.7808 (tpp) REVERT: B 195 LYS cc_start: 0.7459 (mmmt) cc_final: 0.7224 (mmmt) REVERT: B 199 TYR cc_start: 0.8250 (p90) cc_final: 0.7947 (p90) REVERT: G 43 ASN cc_start: 0.8549 (t0) cc_final: 0.8310 (t0) REVERT: G 109 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: H 112 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8758 (p) outliers start: 67 outliers final: 46 residues processed: 221 average time/residue: 0.0878 time to fit residues: 30.5388 Evaluate side-chains 197 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 170 PHE 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 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 327 GLU 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 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 277 THR Chi-restraints excluded: chain H residue 288 THR 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: 0.0670 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 132 optimal weight: 0.0270 chunk 133 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 149 ASN A 230 HIS B 174 HIS G 246 ASN H 71 HIS H 169 HIS ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.146918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.110105 restraints weight = 15845.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.108846 restraints weight = 13993.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.110749 restraints weight = 15119.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110475 restraints weight = 10219.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.110690 restraints weight = 9797.336| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13088 Z= 0.105 Angle : 0.563 6.690 17846 Z= 0.294 Chirality : 0.045 0.209 1974 Planarity : 0.004 0.050 2288 Dihedral : 5.214 59.331 1771 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.53 % Allowed : 15.82 % Favored : 78.65 % 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 are not related in a simple way. whole: -2.22 (0.20), residues: 1630 helix: -1.10 (0.62), residues: 72 sheet: -1.32 (0.22), residues: 538 loop : -1.62 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.015 0.001 TYR H 165 PHE 0.009 0.001 PHE B 15 TRP 0.007 0.001 TRP B 279 HIS 0.013 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13054) covalent geometry : angle 0.55617 / 0.29 (17778) SS BOND : bond 0.00263 / 0.17 ( 34) SS BOND : angle 1.52240 / 1.03 ( 68) hydrogen bonds : bond 0.03008 / 1.95 ( 274) hydrogen bonds : angle 5.99040 / 4.08 ( 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 239 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 161 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 407 TRP cc_start: 0.7011 (OUTLIER) cc_final: 0.6386 (m-10) REVERT: B 8 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8855 (pp) REVERT: B 195 LYS cc_start: 0.7454 (mmmt) cc_final: 0.7167 (mmmt) REVERT: B 199 TYR cc_start: 0.8337 (p90) cc_final: 0.7875 (p90) REVERT: G 102 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: G 109 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: H 112 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8730 (p) outliers start: 78 outliers final: 50 residues processed: 222 average time/residue: 0.0869 time to fit residues: 30.4293 Evaluate side-chains 203 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 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 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 273 THR 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 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 124 VAL 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 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 78 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 166 ILE 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 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: 3.9990 chunk 57 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 345 HIS G 246 ASN H 71 HIS ** H 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.145334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109061 restraints weight = 16006.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106716 restraints weight = 14862.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108568 restraints weight = 15479.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108552 restraints weight = 10241.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.108722 restraints weight = 10941.019| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13088 Z= 0.135 Angle : 0.585 7.472 17846 Z= 0.303 Chirality : 0.046 0.172 1974 Planarity : 0.004 0.048 2288 Dihedral : 5.075 58.880 1769 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 6.17 % Allowed : 15.74 % Favored : 78.09 % 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 are not related in a simple way. whole: -2.12 (0.20), residues: 1630 helix: -1.05 (0.63), residues: 72 sheet: -1.22 (0.22), residues: 538 loop : -1.57 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.017 0.001 TYR H 165 PHE 0.013 0.001 PHE A 51 TRP 0.007 0.001 TRP B 279 HIS 0.005 0.001 HIS H 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (13054) covalent geometry : angle 0.57763 / 0.30 (17778) SS BOND : bond 0.00291 / 0.20 ( 34) SS BOND : angle 1.59342 / 1.07 ( 68) hydrogen bonds : bond 0.03090 / 2.00 ( 274) hydrogen bonds : angle 5.88264 / 4.01 ( 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 246 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 159 time to evaluate : 0.407 Fit side-chains REVERT: A 407 TRP cc_start: 0.7030 (OUTLIER) cc_final: 0.6387 (m-10) REVERT: B 8 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8904 (pp) REVERT: B 195 LYS cc_start: 0.7490 (mmmt) cc_final: 0.7181 (mmmt) REVERT: G 102 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8638 (tt0) REVERT: G 109 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: G 275 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7718 (m170) REVERT: H 55 GLN cc_start: 0.7617 (tt0) cc_final: 0.7385 (tt0) outliers start: 87 outliers final: 60 residues processed: 228 average time/residue: 0.0895 time to fit residues: 31.6840 Evaluate side-chains 213 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 148 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 100 ASN 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 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 229 ILE 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 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 283 ILE 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 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 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 275 HIS 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 86 SER Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 166 ILE 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 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: 0.9980 chunk 139 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 0.0270 chunk 35 optimal weight: 0.0070 chunk 77 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN G 246 ASN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.147164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.110445 restraints weight = 15833.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.109348 restraints weight = 14086.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.110808 restraints weight = 14766.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.111035 restraints weight = 10037.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.111124 restraints weight = 10397.819| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13088 Z= 0.101 Angle : 0.554 6.951 17846 Z= 0.288 Chirality : 0.044 0.171 1974 Planarity : 0.004 0.044 2288 Dihedral : 4.906 58.581 1769 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.39 % Allowed : 16.67 % 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 are not related in a simple way. whole: -2.00 (0.21), residues: 1630 helix: -1.07 (0.62), residues: 72 sheet: -1.13 (0.22), residues: 542 loop : -1.47 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.017 0.001 TYR A 15 PHE 0.009 0.001 PHE B 64 TRP 0.007 0.001 TRP B 279 HIS 0.015 0.001 HIS G 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (13054) covalent geometry : angle 0.54825 / 0.29 (17778) SS BOND : bond 0.00257 / 0.18 ( 34) SS BOND : angle 1.40645 / 0.94 ( 68) hydrogen bonds : bond 0.02778 / 1.81 ( 274) hydrogen bonds : angle 5.67446 / 3.87 ( 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 242 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 166 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 407 TRP cc_start: 0.7080 (OUTLIER) cc_final: 0.6456 (m-10) REVERT: B 8 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8924 (pp) REVERT: G 102 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: G 109 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7139 (pt0) REVERT: G 252 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7867 (mm110) REVERT: G 275 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7634 (m170) REVERT: G 372 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7423 (mmmt) REVERT: H 55 GLN cc_start: 0.7603 (tt0) cc_final: 0.7266 (tt0) REVERT: H 112 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8756 (p) outliers start: 76 outliers final: 55 residues processed: 225 average time/residue: 0.0891 time to fit residues: 31.4066 Evaluate side-chains 214 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 100 ASN 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 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 229 ILE 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 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 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 34 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 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 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 275 HIS 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 330 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 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 252 GLN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 246 ASN H 71 HIS ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.144632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.106432 restraints weight = 15832.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.107206 restraints weight = 13913.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.107811 restraints weight = 13171.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108233 restraints weight = 9196.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.108512 restraints weight = 8822.664| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13088 Z= 0.154 Angle : 0.593 6.713 17846 Z= 0.307 Chirality : 0.046 0.264 1974 Planarity : 0.005 0.098 2288 Dihedral : 5.023 56.966 1769 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.24 % Allowed : 16.45 % 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 are not related in a simple way. whole: -2.02 (0.21), residues: 1630 helix: -1.06 (0.62), residues: 72 sheet: -1.10 (0.22), residues: 548 loop : -1.52 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 216 TYR 0.018 0.001 TYR A 15 PHE 0.015 0.001 PHE A 51 TRP 0.007 0.001 TRP B 279 HIS 0.011 0.001 HIS G 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.15 (13054) covalent geometry : angle 0.58568 / 0.30 (17778) SS BOND : bond 0.00302 / 0.20 ( 34) SS BOND : angle 1.58624 / 1.07 ( 68) hydrogen bonds : bond 0.03061 / 1.99 ( 274) hydrogen bonds : angle 5.68086 / 3.88 ( 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 244 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 156 time to evaluate : 0.544 Fit side-chains REVERT: A 252 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: A 407 TRP cc_start: 0.7068 (OUTLIER) cc_final: 0.6414 (m-10) REVERT: B 8 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8970 (pp) REVERT: B 199 TYR cc_start: 0.8456 (p90) cc_final: 0.7948 (p90) REVERT: G 109 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7215 (pt0) REVERT: G 252 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7920 (mm110) REVERT: G 372 LYS cc_start: 0.7850 (mmtm) cc_final: 0.7458 (mmmt) REVERT: H 55 GLN cc_start: 0.7719 (tt0) cc_final: 0.7393 (tt0) outliers start: 88 outliers final: 70 residues processed: 227 average time/residue: 0.0862 time to fit residues: 30.7706 Evaluate side-chains 223 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 148 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 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 229 ILE Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 297 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 8 LEU Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 85 ILE 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 302 LEU 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 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 15 optimal weight: 0.0010 chunk 128 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN G 246 ASN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.144214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.109858 restraints weight = 15630.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108692 restraints weight = 18306.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.109960 restraints weight = 17833.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.109801 restraints weight = 13010.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.110239 restraints weight = 14046.081| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13088 Z= 0.167 Angle : 0.612 7.028 17846 Z= 0.317 Chirality : 0.047 0.180 1974 Planarity : 0.004 0.085 2288 Dihedral : 5.151 55.383 1769 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.88 % Allowed : 15.96 % Favored : 77.16 % 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 are not related in a simple way. whole: -2.02 (0.21), residues: 1630 helix: -1.04 (0.62), residues: 72 sheet: -1.08 (0.22), residues: 548 loop : -1.54 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.018 0.002 TYR A 15 PHE 0.015 0.001 PHE A 51 TRP 0.009 0.001 TRP G 89 HIS 0.014 0.001 HIS G 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (13054) covalent geometry : angle 0.60445 / 0.31 (17778) SS BOND : bond 0.00309 / 0.20 ( 34) SS BOND : angle 1.63756 / 1.12 ( 68) hydrogen bonds : bond 0.03190 / 2.06 ( 274) hydrogen bonds : angle 5.71109 / 3.90 ( 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 240 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 143 time to evaluate : 0.365 Fit side-chains REVERT: A 252 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: A 407 TRP cc_start: 0.6971 (OUTLIER) cc_final: 0.6205 (m-10) REVERT: B 8 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9006 (pp) REVERT: B 18 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: B 199 TYR cc_start: 0.8458 (p90) cc_final: 0.8070 (p90) REVERT: G 109 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: G 220 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.9012 (ptp-110) REVERT: G 252 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8125 (mm110) REVERT: H 55 GLN cc_start: 0.7683 (tt0) cc_final: 0.7373 (tt0) REVERT: H 187 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7785 (p) outliers start: 97 outliers final: 73 residues processed: 226 average time/residue: 0.0872 time to fit residues: 30.6569 Evaluate side-chains 225 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 144 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 177 VAL 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 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 297 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 8 LEU Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 85 ILE 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 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 315 THR 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 34 VAL 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 154 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 0.0270 chunk 139 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 ASN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.143577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.109363 restraints weight = 15741.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107508 restraints weight = 22605.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.109135 restraints weight = 21772.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.109154 restraints weight = 14268.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109663 restraints weight = 14222.818| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13088 Z= 0.177 Angle : 0.627 8.982 17846 Z= 0.323 Chirality : 0.047 0.278 1974 Planarity : 0.004 0.081 2288 Dihedral : 5.232 54.051 1769 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.52 % Allowed : 16.38 % 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 are not related in a simple way. whole: -2.04 (0.21), residues: 1630 helix: -1.08 (0.60), residues: 72 sheet: -1.05 (0.22), residues: 546 loop : -1.58 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.018 0.002 TYR H 165 PHE 0.015 0.001 PHE A 51 TRP 0.009 0.001 TRP G 89 HIS 0.013 0.001 HIS G 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (13054) covalent geometry : angle 0.61991 / 0.32 (17778) SS BOND : bond 0.00320 / 0.21 ( 34) SS BOND : angle 1.66215 / 1.14 ( 68) hydrogen bonds : bond 0.03231 / 2.08 ( 274) hydrogen bonds : angle 5.75220 / 3.93 ( 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 248 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 156 time to evaluate : 0.496 Fit side-chains REVERT: A 252 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: A 407 TRP cc_start: 0.6978 (OUTLIER) cc_final: 0.6299 (m-10) REVERT: B 8 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9025 (pp) REVERT: B 18 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: B 199 TYR cc_start: 0.8462 (p90) cc_final: 0.8113 (p90) REVERT: G 220 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.9012 (ptp-110) REVERT: G 252 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8142 (mm110) REVERT: G 298 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6284 (tm-30) REVERT: G 372 LYS cc_start: 0.7901 (mmtm) cc_final: 0.7520 (mmmt) REVERT: H 187 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7815 (p) REVERT: N 89 TRP cc_start: 0.5829 (m-10) cc_final: 0.5568 (m-10) outliers start: 92 outliers final: 80 residues processed: 234 average time/residue: 0.0970 time to fit residues: 34.7189 Evaluate side-chains 234 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 147 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 297 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 8 LEU Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 85 ILE 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 296 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR 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 18 LEU 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 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 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 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 252 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.146853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.112780 restraints weight = 15743.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.111577 restraints weight = 22055.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.113298 restraints weight = 20321.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.113117 restraints weight = 13415.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.113628 restraints weight = 12715.292| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13088 Z= 0.111 Angle : 0.570 8.430 17846 Z= 0.293 Chirality : 0.045 0.239 1974 Planarity : 0.004 0.077 2288 Dihedral : 4.918 53.691 1769 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.60 % Allowed : 17.45 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.21), residues: 1630 helix: -0.98 (0.62), residues: 72 sheet: -0.87 (0.23), residues: 526 loop : -1.50 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.018 0.001 TYR B 328 PHE 0.009 0.001 PHE H 64 TRP 0.008 0.001 TRP B 279 HIS 0.013 0.001 HIS G 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (13054) covalent geometry : angle 0.56424 / 0.29 (17778) SS BOND : bond 0.00265 / 0.17 ( 34) SS BOND : angle 1.38388 / 0.94 ( 68) hydrogen bonds : bond 0.02779 / 1.81 ( 274) hydrogen bonds : angle 5.49091 / 3.75 ( 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 232 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 153 time to evaluate : 0.506 Fit side-chains REVERT: A 204 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: A 407 TRP cc_start: 0.7028 (OUTLIER) cc_final: 0.6366 (m-10) REVERT: B 8 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9003 (pp) REVERT: B 199 TYR cc_start: 0.8344 (p90) cc_final: 0.7986 (p90) REVERT: G 102 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: G 109 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7117 (pt0) REVERT: G 220 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8964 (ptp-110) REVERT: G 242 MET cc_start: 0.7452 (tpt) cc_final: 0.7159 (tpt) REVERT: G 252 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7738 (mm110) REVERT: G 298 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6269 (tm-30) REVERT: G 372 LYS cc_start: 0.7853 (mmtm) cc_final: 0.7545 (mmmt) REVERT: H 55 GLN cc_start: 0.7564 (tt0) cc_final: 0.7275 (tt0) REVERT: H 187 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7811 (p) outliers start: 79 outliers final: 64 residues processed: 219 average time/residue: 0.0950 time to fit residues: 32.0057 Evaluate side-chains 220 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 148 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 100 ASN 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 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 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 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 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 LEU 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 B residue 338 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 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 220 ARG 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 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 252 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN G 43 ASN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.148468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.115400 restraints weight = 15652.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.114334 restraints weight = 20633.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.115642 restraints weight = 19164.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.115545 restraints weight = 13721.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.115917 restraints weight = 14837.751| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13088 Z= 0.100 Angle : 0.558 8.317 17846 Z= 0.288 Chirality : 0.044 0.170 1974 Planarity : 0.004 0.077 2288 Dihedral : 4.754 53.408 1769 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.82 % Allowed : 18.51 % Favored : 76.67 % 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 are not related in a simple way. whole: -1.76 (0.21), residues: 1630 helix: -0.94 (0.62), residues: 72 sheet: -0.80 (0.23), residues: 530 loop : -1.41 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.018 0.001 TYR A 15 PHE 0.010 0.001 PHE B 64 TRP 0.007 0.001 TRP A 243 HIS 0.013 0.001 HIS G 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (13054) covalent geometry : angle 0.55282 / 0.29 (17778) SS BOND : bond 0.00243 / 0.16 ( 34) SS BOND : angle 1.30683 / 0.89 ( 68) hydrogen bonds : bond 0.02619 / 1.73 ( 274) hydrogen bonds : angle 5.33652 / 3.64 ( 687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2137.88 seconds wall clock time: 37 minutes 46.27 seconds (2266.27 seconds total)