Starting phenix.real_space_refine on Wed Jul 30 17:53:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l99_62898/07_2025/9l99_62898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l99_62898/07_2025/9l99_62898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l99_62898/07_2025/9l99_62898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l99_62898/07_2025/9l99_62898.map" model { file = "/net/cci-nas-00/data/ceres_data/9l99_62898/07_2025/9l99_62898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l99_62898/07_2025/9l99_62898.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12710 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3122 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 27, 'TRANS': 383} Chain: "B" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2929 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 25, 'TRANS': 343} Chain: "G" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3122 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 27, 'TRANS': 383} Chain: "H" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2929 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 25, 'TRANS': 343} Chain: "N" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.98, per 1000 atoms: 0.55 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: 2.52 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.52 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: 3.38 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4124 1.35 - 1.48: 3366 1.48 - 1.61: 5466 1.61 - 1.74: 0 1.74 - 1.86: 98 Bond restraints: 13054 Sorted by residual: bond pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CA CYS H 226 " pdb=" CB CYS H 226 " ideal model delta sigma weight residual 1.533 1.507 0.026 1.65e-02 3.67e+03 2.52e+00 bond pdb=" CB GLU G 298 " pdb=" CG GLU G 298 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CB ASN A 139 " pdb=" CG ASN A 139 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.13e+00 bond pdb=" CG PRO A 265 " pdb=" CD PRO A 265 " ideal model delta sigma weight residual 1.503 1.454 0.049 3.40e-02 8.65e+02 2.06e+00 ... (remaining 13049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 17461 2.17 - 4.34: 282 4.34 - 6.51: 26 6.51 - 8.68: 7 8.68 - 10.85: 2 Bond angle restraints: 17778 Sorted by residual: angle pdb=" CA CYS H 226 " pdb=" CB CYS H 226 " pdb=" SG CYS H 226 " ideal model delta sigma weight residual 114.40 125.25 -10.85 2.30e+00 1.89e-01 2.23e+01 angle pdb=" N VAL A 148 " pdb=" CA VAL A 148 " pdb=" C VAL A 148 " ideal model delta sigma weight residual 112.90 108.79 4.11 9.60e-01 1.09e+00 1.83e+01 angle pdb=" CA GLN A 93 " pdb=" C GLN A 93 " pdb=" N CYS A 94 " ideal model delta sigma weight residual 118.43 123.71 -5.28 1.33e+00 5.65e-01 1.58e+01 angle pdb=" CA CYS H 201 " pdb=" CB CYS H 201 " pdb=" SG CYS H 201 " ideal model delta sigma weight residual 114.40 123.26 -8.86 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CA LYS B 202 " pdb=" CB LYS B 202 " pdb=" CG LYS B 202 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 ... (remaining 17773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 7109 18.01 - 36.02: 604 36.02 - 54.02: 121 54.02 - 72.03: 22 72.03 - 90.04: 12 Dihedral angle restraints: 7868 sinusoidal: 3109 harmonic: 4759 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 124 " pdb=" CB CYS B 124 " ideal model delta sinusoidal sigma weight residual 93.00 -177.71 -89.29 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS N 79 " pdb=" SG CYS N 79 " pdb=" SG CYS N 97 " pdb=" CB CYS N 97 " ideal model delta sinusoidal sigma weight residual 93.00 172.56 -79.56 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS H 203 " pdb=" SG CYS H 203 " pdb=" SG CYS H 220 " pdb=" CB CYS H 220 " ideal model delta sinusoidal sigma weight residual -86.00 -161.31 75.31 1 1.00e+01 1.00e-02 7.17e+01 ... (remaining 7865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1338 0.039 - 0.077: 429 0.077 - 0.116: 165 0.116 - 0.155: 37 0.155 - 0.193: 5 Chirality restraints: 1974 Sorted by residual: chirality pdb=" CG LEU G 18 " pdb=" CB LEU G 18 " pdb=" CD1 LEU G 18 " pdb=" CD2 LEU G 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA CYS H 226 " pdb=" N CYS H 226 " pdb=" C CYS H 226 " pdb=" CB CYS H 226 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CB THR G 126 " pdb=" CA THR G 126 " pdb=" OG1 THR G 126 " pdb=" CG2 THR G 126 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 1971 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 264 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 265 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 298 " -0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CD GLU G 298 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU G 298 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU G 298 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 298 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C GLU G 298 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU G 298 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL G 299 " -0.014 2.00e-02 2.50e+03 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 532 2.71 - 3.26: 11844 3.26 - 3.81: 18720 3.81 - 4.35: 22128 4.35 - 4.90: 39722 Nonbonded interactions: 92946 Sorted by model distance: nonbonded pdb=" O TRP N 89 " pdb="CA CA N 202 " model vdw 2.164 2.510 nonbonded pdb=" O ASP G 385 " pdb=" NE2 GLN H 341 " model vdw 2.212 3.120 nonbonded pdb=" O PHE B 26 " pdb=" OH TYR B 69 " model vdw 2.218 3.040 nonbonded pdb=" OG SER G 309 " pdb=" OE1 GLN H 341 " model vdw 2.232 3.040 nonbonded pdb=" O ASP A 385 " pdb=" NE2 GLN B 341 " model vdw 2.246 3.120 ... (remaining 92941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.690 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13088 Z= 0.152 Angle : 0.681 10.852 17846 Z= 0.379 Chirality : 0.045 0.193 1974 Planarity : 0.005 0.107 2288 Dihedral : 13.546 90.041 4710 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP B 279 HIS 0.005 0.001 HIS H 169 PHE 0.021 0.001 PHE G 95 TYR 0.014 0.001 TYR A 308 ARG 0.004 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.28358 ( 274) hydrogen bonds : angle 10.35360 ( 687) SS BOND : bond 0.00358 ( 34) SS BOND : angle 2.31329 ( 68) covalent geometry : bond 0.00333 (13054) covalent geometry : angle 0.66756 (17778) *********************** 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 : 1.426 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: 0.2259 time to fit residues: 55.2137 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 : 1.436 ------------------------------------------------------------------------------- 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 136 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 77 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 230 HIS A 333 HIS A 345 HIS A 392 HIS B 96 HIS B 153 HIS B 174 HIS B 246 HIS G 43 ASN G 246 ASN G 275 HIS ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN H 246 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.143371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.106312 restraints weight = 15733.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.104382 restraints weight = 13509.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105910 restraints weight = 14661.524| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13088 Z= 0.203 Angle : 0.675 8.775 17846 Z= 0.353 Chirality : 0.049 0.178 1974 Planarity : 0.005 0.075 2288 Dihedral : 5.766 58.101 1771 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 5.25 % Allowed : 13.62 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.20), residues: 1630 helix: -1.17 (0.62), residues: 72 sheet: -1.75 (0.21), residues: 552 loop : -1.86 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.008 0.001 HIS A 230 PHE 0.016 0.001 PHE A 51 TYR 0.018 0.002 TYR H 165 ARG 0.004 0.001 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 274) hydrogen bonds : angle 7.03046 ( 687) SS BOND : bond 0.00353 ( 34) SS BOND : angle 2.00704 ( 68) covalent geometry : bond 0.00508 (13054) covalent geometry : angle 0.66525 (17778) *********************** 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 242 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 168 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 407 TRP cc_start: 0.6749 (OUTLIER) cc_final: 0.6273 (m-10) REVERT: B 37 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7544 (mt-10) REVERT: B 199 TYR cc_start: 0.8261 (p90) cc_final: 0.7919 (p90) REVERT: G 43 ASN cc_start: 0.8523 (t0) cc_final: 0.8207 (t0) REVERT: H 197 VAL cc_start: 0.8472 (m) cc_final: 0.8267 (m) outliers start: 74 outliers final: 48 residues processed: 228 average time/residue: 0.2024 time to fit residues: 70.2570 Evaluate side-chains 203 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 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 G residue 7 VAL Chi-restraints excluded: chain G residue 47 VAL 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 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 367 VAL Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 128 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 214 GLN G 125 HIS G 246 ASN G 275 HIS ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.145712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.108851 restraints weight = 15870.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.107168 restraints weight = 13982.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108083 restraints weight = 16998.102| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13088 Z= 0.131 Angle : 0.601 7.522 17846 Z= 0.314 Chirality : 0.046 0.174 1974 Planarity : 0.004 0.053 2288 Dihedral : 5.477 57.828 1771 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.04 % Allowed : 14.96 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1630 helix: -1.07 (0.63), residues: 72 sheet: -1.54 (0.21), residues: 552 loop : -1.73 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 279 HIS 0.006 0.001 HIS A 230 PHE 0.012 0.001 PHE A 51 TYR 0.016 0.001 TYR H 165 ARG 0.003 0.000 ARG H 20 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 274) hydrogen bonds : angle 6.43981 ( 687) SS BOND : bond 0.00311 ( 34) SS BOND : angle 1.70736 ( 68) covalent geometry : bond 0.00324 (13054) covalent geometry : angle 0.59238 (17778) *********************** 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 233 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 162 time to evaluate : 1.303 Fit side-chains REVERT: A 231 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 407 TRP cc_start: 0.6890 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: B 195 LYS cc_start: 0.7470 (mmmt) cc_final: 0.7247 (mmmt) REVERT: B 199 TYR cc_start: 0.8346 (p90) cc_final: 0.7891 (p90) REVERT: G 43 ASN cc_start: 0.8553 (t0) cc_final: 0.8303 (t0) REVERT: G 109 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7337 (pt0) outliers start: 71 outliers final: 50 residues processed: 218 average time/residue: 0.1904 time to fit residues: 64.9134 Evaluate side-chains 201 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 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 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 65 SER Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 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 49 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 HIS G 246 ASN G 275 HIS ** H 169 HIS ** 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 = 0.3496 r_free = 0.3496 target = 0.143989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.109733 restraints weight = 15611.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.108328 restraints weight = 23437.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.109525 restraints weight = 24845.553| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13088 Z= 0.177 Angle : 0.631 7.439 17846 Z= 0.328 Chirality : 0.047 0.207 1974 Planarity : 0.004 0.054 2288 Dihedral : 5.536 59.323 1771 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 6.88 % Allowed : 14.33 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.20), residues: 1630 helix: -1.17 (0.61), residues: 72 sheet: -1.39 (0.22), residues: 546 loop : -1.74 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 279 HIS 0.004 0.001 HIS A 52 PHE 0.015 0.001 PHE A 51 TYR 0.020 0.002 TYR H 165 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 274) hydrogen bonds : angle 6.20155 ( 687) SS BOND : bond 0.00316 ( 34) SS BOND : angle 1.79372 ( 68) covalent geometry : bond 0.00444 (13054) covalent geometry : angle 0.62255 (17778) *********************** 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 250 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 153 time to evaluate : 1.386 Fit side-chains REVERT: A 407 TRP cc_start: 0.7130 (OUTLIER) cc_final: 0.6489 (m-10) REVERT: B 8 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8970 (pp) REVERT: B 195 LYS cc_start: 0.7630 (mmmt) cc_final: 0.7351 (mmmt) REVERT: B 199 TYR cc_start: 0.8411 (p90) cc_final: 0.7944 (p90) REVERT: G 43 ASN cc_start: 0.8630 (t0) cc_final: 0.8255 (t0) outliers start: 97 outliers final: 71 residues processed: 231 average time/residue: 0.2028 time to fit residues: 72.1331 Evaluate side-chains 217 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 144 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 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 7 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 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 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN G 246 ASN G 275 HIS ** H 169 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.145021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.109769 restraints weight = 15680.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.107948 restraints weight = 18833.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109290 restraints weight = 17968.695| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13088 Z= 0.140 Angle : 0.598 7.879 17846 Z= 0.310 Chirality : 0.046 0.172 1974 Planarity : 0.004 0.048 2288 Dihedral : 5.257 58.375 1769 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 6.17 % Allowed : 15.96 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.20), residues: 1630 helix: -1.09 (0.62), residues: 72 sheet: -1.26 (0.22), residues: 544 loop : -1.67 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 243 HIS 0.014 0.001 HIS G 331 PHE 0.013 0.001 PHE A 51 TYR 0.017 0.001 TYR H 165 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 274) hydrogen bonds : angle 5.98815 ( 687) SS BOND : bond 0.00285 ( 34) SS BOND : angle 1.66589 ( 68) covalent geometry : bond 0.00349 (13054) covalent geometry : angle 0.59039 (17778) *********************** 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 : 1.429 Fit side-chains REVERT: A 407 TRP cc_start: 0.7109 (OUTLIER) cc_final: 0.6484 (m-10) REVERT: B 8 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8944 (pp) REVERT: B 195 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7319 (mmmt) REVERT: B 199 TYR cc_start: 0.8408 (p90) cc_final: 0.7961 (p90) REVERT: G 43 ASN cc_start: 0.8544 (t0) cc_final: 0.8219 (t0) REVERT: G 109 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7303 (pt0) outliers start: 87 outliers final: 67 residues processed: 233 average time/residue: 0.2224 time to fit residues: 79.9525 Evaluate side-chains 218 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 148 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 170 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 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 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 124 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 ASN ** H 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.143769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.110081 restraints weight = 15852.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.108407 restraints weight = 21943.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.110017 restraints weight = 20973.767| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13088 Z= 0.168 Angle : 0.619 8.354 17846 Z= 0.321 Chirality : 0.047 0.174 1974 Planarity : 0.004 0.049 2288 Dihedral : 5.304 56.443 1769 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 7.45 % Allowed : 14.96 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1630 helix: -1.11 (0.61), residues: 72 sheet: -1.24 (0.22), residues: 548 loop : -1.66 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.011 0.001 HIS G 331 PHE 0.013 0.001 PHE A 51 TYR 0.022 0.002 TYR A 46 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 274) hydrogen bonds : angle 5.91519 ( 687) SS BOND : bond 0.00321 ( 34) SS BOND : angle 1.75045 ( 68) covalent geometry : bond 0.00422 (13054) covalent geometry : angle 0.61080 (17778) *********************** 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 265 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 160 time to evaluate : 1.401 Fit side-chains REVERT: A 204 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8339 (mt0) REVERT: A 252 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: A 407 TRP cc_start: 0.7197 (OUTLIER) cc_final: 0.6535 (m-10) REVERT: B 8 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8991 (pp) REVERT: B 18 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: B 195 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7371 (mmmt) REVERT: B 199 TYR cc_start: 0.8406 (p90) cc_final: 0.8014 (p90) REVERT: G 109 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: G 252 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8098 (mm110) outliers start: 105 outliers final: 78 residues processed: 250 average time/residue: 0.2017 time to fit residues: 77.4288 Evaluate side-chains 237 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 152 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 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 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 127 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.144737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.109739 restraints weight = 15673.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.108099 restraints weight = 19719.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.110140 restraints weight = 18843.026| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13088 Z= 0.143 Angle : 0.597 8.442 17846 Z= 0.309 Chirality : 0.046 0.255 1974 Planarity : 0.004 0.045 2288 Dihedral : 5.157 55.328 1769 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 6.60 % Allowed : 15.60 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.21), residues: 1630 helix: -1.06 (0.62), residues: 72 sheet: -1.12 (0.22), residues: 544 loop : -1.60 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 279 HIS 0.014 0.001 HIS G 331 PHE 0.013 0.001 PHE A 51 TYR 0.019 0.001 TYR A 46 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 274) hydrogen bonds : angle 5.75740 ( 687) SS BOND : bond 0.00295 ( 34) SS BOND : angle 1.59778 ( 68) covalent geometry : bond 0.00358 (13054) covalent geometry : angle 0.59012 (17778) *********************** 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 251 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 158 time to evaluate : 1.299 Fit side-chains REVERT: A 204 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: A 252 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8845 (mm-40) REVERT: A 407 TRP cc_start: 0.6877 (OUTLIER) cc_final: 0.6206 (m-10) REVERT: B 8 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8980 (pp) REVERT: B 195 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7285 (mmmt) REVERT: B 199 TYR cc_start: 0.8373 (p90) cc_final: 0.7965 (p90) REVERT: G 109 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: G 220 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.9014 (ptp-110) REVERT: G 252 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7854 (mm110) REVERT: G 298 GLU cc_start: 0.6707 (tm-30) cc_final: 0.6232 (tm-30) REVERT: N 89 TRP cc_start: 0.6090 (m-10) cc_final: 0.5839 (m-10) outliers start: 93 outliers final: 75 residues processed: 237 average time/residue: 0.2093 time to fit residues: 75.4428 Evaluate side-chains 232 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 150 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 35 SER 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 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 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 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 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 376 CYS Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 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 88 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.144578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.109322 restraints weight = 15761.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.107361 restraints weight = 18839.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.110125 restraints weight = 18108.643| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13088 Z= 0.149 Angle : 0.604 8.742 17846 Z= 0.311 Chirality : 0.046 0.209 1974 Planarity : 0.005 0.102 2288 Dihedral : 5.147 54.654 1769 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.74 % Allowed : 15.89 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.20), residues: 1630 helix: -1.07 (0.61), residues: 72 sheet: -1.09 (0.22), residues: 544 loop : -1.60 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 279 HIS 0.012 0.001 HIS G 331 PHE 0.012 0.001 PHE A 51 TYR 0.020 0.001 TYR A 46 ARG 0.002 0.000 ARG G 216 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 274) hydrogen bonds : angle 5.72121 ( 687) SS BOND : bond 0.00300 ( 34) SS BOND : angle 1.59888 ( 68) covalent geometry : bond 0.00377 (13054) covalent geometry : angle 0.59734 (17778) *********************** 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 246 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 151 time to evaluate : 1.299 Fit side-chains REVERT: A 252 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: A 407 TRP cc_start: 0.6905 (OUTLIER) cc_final: 0.6238 (m-10) REVERT: B 8 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8971 (pp) REVERT: B 195 LYS cc_start: 0.7577 (mmmt) cc_final: 0.7264 (mmmt) REVERT: B 199 TYR cc_start: 0.8473 (p90) cc_final: 0.8048 (p90) REVERT: G 43 ASN cc_start: 0.8545 (t0) cc_final: 0.8295 (t0) REVERT: G 109 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: G 220 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.9048 (ptp-110) REVERT: G 252 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7878 (mm110) REVERT: G 298 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6267 (tm-30) REVERT: G 372 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7505 (mmmt) REVERT: H 187 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7754 (p) REVERT: N 89 TRP cc_start: 0.6129 (m-10) cc_final: 0.5878 (m-10) outliers start: 95 outliers final: 85 residues processed: 231 average time/residue: 0.2104 time to fit residues: 73.6632 Evaluate side-chains 241 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 149 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 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 311 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 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 327 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 71 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.142657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107771 restraints weight = 15812.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.105744 restraints weight = 19932.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.106967 restraints weight = 19465.359| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13088 Z= 0.194 Angle : 0.645 9.482 17846 Z= 0.332 Chirality : 0.048 0.180 1974 Planarity : 0.005 0.095 2288 Dihedral : 5.334 53.657 1769 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 7.16 % Allowed : 15.82 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.20), residues: 1630 helix: -1.14 (0.60), residues: 72 sheet: -1.11 (0.22), residues: 546 loop : -1.64 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 89 HIS 0.011 0.001 HIS G 331 PHE 0.014 0.001 PHE A 51 TYR 0.022 0.002 TYR A 46 ARG 0.003 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 274) hydrogen bonds : angle 5.81963 ( 687) SS BOND : bond 0.00347 ( 34) SS BOND : angle 1.74355 ( 68) covalent geometry : bond 0.00493 (13054) covalent geometry : angle 0.63750 (17778) *********************** 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 260 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 159 time to evaluate : 1.463 Fit side-chains REVERT: A 252 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: A 407 TRP cc_start: 0.7099 (OUTLIER) cc_final: 0.6384 (m-10) REVERT: B 18 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: B 195 LYS cc_start: 0.7611 (mmmt) cc_final: 0.7305 (mmmt) REVERT: B 199 TYR cc_start: 0.8492 (p90) cc_final: 0.8100 (p90) REVERT: G 220 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.7252 (ptp90) REVERT: G 252 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8146 (mm110) REVERT: G 298 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6454 (tm-30) REVERT: G 372 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7597 (mmmt) REVERT: G 381 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7227 (mptt) REVERT: H 187 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7808 (p) REVERT: N 89 TRP cc_start: 0.6119 (m-10) cc_final: 0.5830 (m-10) outliers start: 101 outliers final: 87 residues processed: 244 average time/residue: 0.2124 time to fit residues: 78.3084 Evaluate side-chains 248 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 155 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 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 321 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 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 260 ARG Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 56 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.147062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.112931 restraints weight = 15687.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.111200 restraints weight = 21817.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.112606 restraints weight = 22727.378| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13088 Z= 0.104 Angle : 0.566 8.536 17846 Z= 0.293 Chirality : 0.045 0.259 1974 Planarity : 0.004 0.088 2288 Dihedral : 4.904 53.645 1769 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.18 % Allowed : 17.94 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.21), residues: 1630 helix: -1.01 (0.62), residues: 72 sheet: -1.00 (0.22), residues: 546 loop : -1.52 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.011 0.001 HIS G 331 PHE 0.009 0.001 PHE H 64 TYR 0.019 0.001 TYR A 15 ARG 0.005 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.02739 ( 274) hydrogen bonds : angle 5.48008 ( 687) SS BOND : bond 0.00256 ( 34) SS BOND : angle 1.36827 ( 68) covalent geometry : bond 0.00248 (13054) covalent geometry : angle 0.56073 (17778) ********************** 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 239 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 166 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8009 (mp0) cc_final: 0.7664 (mp0) REVERT: A 69 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7935 (pttp) REVERT: A 252 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: A 407 TRP cc_start: 0.7086 (OUTLIER) cc_final: 0.6406 (m-10) REVERT: B 69 TYR cc_start: 0.8176 (m-80) cc_final: 0.7964 (m-80) REVERT: B 195 LYS cc_start: 0.7628 (mmmt) cc_final: 0.7409 (mmmt) REVERT: B 199 TYR cc_start: 0.8432 (p90) cc_final: 0.8071 (p90) REVERT: G 43 ASN cc_start: 0.8684 (t0) cc_final: 0.8469 (t0) REVERT: G 102 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: G 109 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: G 242 MET cc_start: 0.7461 (tpt) cc_final: 0.7160 (tpt) REVERT: G 252 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7708 (mm110) REVERT: G 298 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6433 (tm-30) REVERT: G 372 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7577 (mmmt) REVERT: H 112 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8772 (p) REVERT: H 187 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7782 (p) REVERT: N 89 TRP cc_start: 0.6143 (m-10) cc_final: 0.5905 (m-10) outliers start: 73 outliers final: 56 residues processed: 226 average time/residue: 0.2091 time to fit residues: 71.7288 Evaluate side-chains 210 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 147 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 114 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 GLN 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 7 THR Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 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 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 148 VAL 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 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 G residue 388 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 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 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 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 139 ASN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.147083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.113053 restraints weight = 15763.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.111197 restraints weight = 21397.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.112567 restraints weight = 20093.550| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13088 Z= 0.114 Angle : 0.576 8.437 17846 Z= 0.296 Chirality : 0.045 0.231 1974 Planarity : 0.004 0.083 2288 Dihedral : 4.831 53.353 1769 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.68 % Allowed : 18.94 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.21), residues: 1630 helix: -0.95 (0.62), residues: 72 sheet: -0.94 (0.23), residues: 546 loop : -1.48 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 279 HIS 0.016 0.001 HIS G 331 PHE 0.010 0.001 PHE H 64 TYR 0.019 0.001 TYR A 15 ARG 0.004 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.02786 ( 274) hydrogen bonds : angle 5.38034 ( 687) SS BOND : bond 0.00249 ( 34) SS BOND : angle 1.38295 ( 68) covalent geometry : bond 0.00281 (13054) covalent geometry : angle 0.57058 (17778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4301.03 seconds wall clock time: 75 minutes 13.04 seconds (4513.04 seconds total)