Starting phenix.real_space_refine on Fri Aug 7 00:25:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ski_54965/08_2026/9ski_54965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ski_54965/08_2026/9ski_54965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ski_54965/08_2026/9ski_54965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ski_54965/08_2026/9ski_54965.map" model { file = "/net/cci-nas-00/data/ceres_data/9ski_54965/08_2026/9ski_54965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ski_54965/08_2026/9ski_54965.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 11337 2.51 5 N 2936 2.21 5 O 3378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17689 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2451 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "C" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "D" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "E" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "F" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "G" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2243 Classifications: {'peptide': 280} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 266} Time building chain proxies: 4.02, per 1000 atoms: 0.23 Number of scatterers: 17689 At special positions: 0 Unit cell: (125.856, 139.932, 177.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 3378 8.00 N 2936 7.00 C 11337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 727.8 milliseconds 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4312 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 7 sheets defined 66.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 39 through 61 removed outlier: 4.061A pdb=" N MET A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.646A pdb=" N SER A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 137 through 150 removed outlier: 4.375A pdb=" N HIS A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 251 removed outlier: 3.639A pdb=" N ILE A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.271A pdb=" N LEU A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 4.052A pdb=" N ARG A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 removed outlier: 4.207A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 42 through 61 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.541A pdb=" N SER B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 124 through 135 removed outlier: 3.580A pdb=" N GLN B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 4.074A pdb=" N HIS B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 251 removed outlier: 3.585A pdb=" N VAL B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.767A pdb=" N SER B 258 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 259 " --> pdb=" O VAL B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 259' Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 337 through 356 removed outlier: 4.161A pdb=" N GLY B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.536A pdb=" N SER C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 140 through 150 removed outlier: 3.795A pdb=" N GLU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 251 removed outlier: 3.627A pdb=" N VAL C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.687A pdb=" N LEU C 294 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 311 removed outlier: 3.500A pdb=" N ARG C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 356 Processing helix chain 'D' and resid 28 through 40 removed outlier: 3.548A pdb=" N LEU D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 59 removed outlier: 3.694A pdb=" N MET D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.761A pdb=" N SER D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 140 through 150 Processing helix chain 'D' and resid 180 through 251 removed outlier: 3.690A pdb=" N VAL D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 286 removed outlier: 3.655A pdb=" N GLU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.521A pdb=" N ARG D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 354 removed outlier: 3.593A pdb=" N ILE D 341 " --> pdb=" O GLY D 337 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 39 through 59 removed outlier: 3.973A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 92 removed outlier: 4.913A pdb=" N LYS E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 113 through 122 Processing helix chain 'E' and resid 124 through 134 Processing helix chain 'E' and resid 140 through 152 removed outlier: 3.849A pdb=" N LYS E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 250 removed outlier: 3.531A pdb=" N THR E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 207 " --> pdb=" O SER E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 295 through 311 removed outlier: 3.516A pdb=" N LYS E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 355 removed outlier: 4.447A pdb=" N VAL E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA E 353 " --> pdb=" O GLY E 349 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS E 354 " --> pdb=" O GLY E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.834A pdb=" N LEU F 32 " --> pdb=" O ASP F 28 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 61 removed outlier: 3.568A pdb=" N VAL F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.597A pdb=" N SER F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 137 through 150 removed outlier: 4.446A pdb=" N HIS F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 249 removed outlier: 3.721A pdb=" N LEU F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 207 " --> pdb=" O SER F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 288 removed outlier: 3.845A pdb=" N LYS F 286 " --> pdb=" O LEU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 294 removed outlier: 3.856A pdb=" N LEU F 294 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 311 removed outlier: 3.530A pdb=" N GLN F 302 " --> pdb=" O LEU F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 356 removed outlier: 3.879A pdb=" N VAL F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 78 Processing helix chain 'G' and resid 79 through 92 removed outlier: 3.517A pdb=" N SER G 85 " --> pdb=" O GLU G 81 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 113 through 124 Processing helix chain 'G' and resid 124 through 134 removed outlier: 3.909A pdb=" N MET G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 151 removed outlier: 3.943A pdb=" N ALA G 144 " --> pdb=" O ASP G 140 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 161 Processing helix chain 'G' and resid 180 through 250 removed outlier: 3.772A pdb=" N LEU G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 207 " --> pdb=" O SER G 203 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS G 219 " --> pdb=" O THR G 215 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 230 " --> pdb=" O ARG G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 288 removed outlier: 3.562A pdb=" N VAL G 288 " --> pdb=" O ILE G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 294 removed outlier: 3.608A pdb=" N LEU G 294 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 311 removed outlier: 3.732A pdb=" N GLN G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 removed outlier: 5.931A pdb=" N VAL A 70 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 152 through 156 removed outlier: 6.174A pdb=" N VAL B 70 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 156 removed outlier: 3.622A pdb=" N VAL C 155 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 70 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 152 through 156 removed outlier: 6.047A pdb=" N VAL D 70 " --> pdb=" O GLN D 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.041A pdb=" N VAL E 70 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 153 through 156 removed outlier: 5.943A pdb=" N VAL F 70 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 152 through 155 removed outlier: 6.587A pdb=" N ALA G 68 " --> pdb=" O PRO G 327 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 325 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR G 72 " --> pdb=" O TYR G 323 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR G 323 " --> pdb=" O THR G 72 " (cutoff:3.500A) 1166 hydrogen bonds defined for protein. 3420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5716 1.34 - 1.46: 3689 1.46 - 1.58: 8512 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 17981 Sorted by residual: bond pdb=" N VAL C 256 " pdb=" CA VAL C 256 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N ASN C 259 " pdb=" CA ASN C 259 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.76e+00 bond pdb=" N SER C 258 " pdb=" CA SER C 258 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.31e-02 5.83e+03 5.27e+00 bond pdb=" N TYR C 257 " pdb=" CA TYR C 257 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.32e-02 5.74e+03 5.06e+00 bond pdb=" N ASP A 93 " pdb=" CA ASP A 93 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.53e+00 ... (remaining 17976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 24099 2.14 - 4.27: 197 4.27 - 6.41: 21 6.41 - 8.55: 7 8.55 - 10.68: 3 Bond angle restraints: 24327 Sorted by residual: angle pdb=" CB LYS C 135 " pdb=" CG LYS C 135 " pdb=" CD LYS C 135 " ideal model delta sigma weight residual 111.30 120.23 -8.93 2.30e+00 1.89e-01 1.51e+01 angle pdb=" N TYR C 257 " pdb=" CA TYR C 257 " pdb=" C TYR C 257 " ideal model delta sigma weight residual 113.16 109.08 4.08 1.24e+00 6.50e-01 1.08e+01 angle pdb=" CA LYS C 135 " pdb=" CB LYS C 135 " pdb=" CG LYS C 135 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CA LEU C 94 " pdb=" CB LEU C 94 " pdb=" CG LEU C 94 " ideal model delta sigma weight residual 116.30 126.98 -10.68 3.50e+00 8.16e-02 9.32e+00 angle pdb=" C ILE B 271 " pdb=" N SER B 272 " pdb=" CA SER B 272 " ideal model delta sigma weight residual 120.82 125.38 -4.56 1.50e+00 4.44e-01 9.23e+00 ... (remaining 24322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9806 17.97 - 35.94: 1016 35.94 - 53.91: 207 53.91 - 71.88: 76 71.88 - 89.85: 19 Dihedral angle restraints: 11124 sinusoidal: 4517 harmonic: 6607 Sorted by residual: dihedral pdb=" CA ASP B 276 " pdb=" C ASP B 276 " pdb=" N GLY B 277 " pdb=" CA GLY B 277 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA TYR E 323 " pdb=" C TYR E 323 " pdb=" N GLN E 324 " pdb=" CA GLN E 324 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TYR G 169 " pdb=" C TYR G 169 " pdb=" N THR G 170 " pdb=" CA THR G 170 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 11121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2031 0.031 - 0.063: 621 0.063 - 0.094: 137 0.094 - 0.125: 68 0.125 - 0.157: 2 Chirality restraints: 2859 Sorted by residual: chirality pdb=" CA VAL C 256 " pdb=" N VAL C 256 " pdb=" C VAL C 256 " pdb=" CB VAL C 256 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA ILE D 98 " pdb=" N ILE D 98 " pdb=" C ILE D 98 " pdb=" CB ILE D 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CG LEU C 139 " pdb=" CB LEU C 139 " pdb=" CD1 LEU C 139 " pdb=" CD2 LEU C 139 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 2856 not shown) Planarity restraints: 3079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 335 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO A 336 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 271 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ILE B 271 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE B 271 " 0.011 2.00e-02 2.50e+03 pdb=" N SER B 272 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 124 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO D 125 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 125 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 125 " 0.021 5.00e-02 4.00e+02 ... (remaining 3076 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1126 2.74 - 3.28: 18587 3.28 - 3.82: 28738 3.82 - 4.36: 33852 4.36 - 4.90: 57466 Nonbonded interactions: 139769 Sorted by model distance: nonbonded pdb=" OD2 ASP G 157 " pdb=" OG1 THR G 173 " model vdw 2.197 3.040 nonbonded pdb=" O LYS G 84 " pdb=" OG1 THR G 87 " model vdw 2.262 3.040 nonbonded pdb=" O ASP G 193 " pdb=" OG1 THR G 197 " model vdw 2.266 3.040 nonbonded pdb=" O LYS A 230 " pdb=" NZ LYS A 230 " model vdw 2.279 3.120 nonbonded pdb=" OD2 ASP C 225 " pdb=" NH1 ARG C 301 " model vdw 2.282 3.120 ... (remaining 139764 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 'B' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'C' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'D' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'E' and (resid 27 through 252 or resid 272 through 356)) selection = (chain 'F' and (resid 27 through 252 or resid 272 through 356)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 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 : 0.002 0.043 17981 Z= 0.113 Angle : 0.482 10.683 24327 Z= 0.252 Chirality : 0.035 0.157 2859 Planarity : 0.004 0.072 3079 Dihedral : 15.977 89.854 6812 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 20.47 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2225 helix: 1.73 (0.14), residues: 1407 sheet: 1.45 (0.42), residues: 174 loop : -1.17 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 100 TYR 0.013 0.001 TYR B 323 PHE 0.006 0.001 PHE A 48 TRP 0.007 0.001 TRP F 37 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (17981) covalent geometry : angle 0.48167 / 0.25 (24327) hydrogen bonds : bond 0.23583 / 15.52 ( 1166) hydrogen bonds : angle 6.35695 / 4.49 ( 3420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 208 ARG cc_start: 0.8470 (mtt90) cc_final: 0.8051 (mtt90) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1695 time to fit residues: 21.8723 Evaluate side-chains 79 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 overall best weight: 2.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN D 248 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 ASN G 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.104914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.066186 restraints weight = 44804.876| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.34 r_work: 0.2932 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17981 Z= 0.265 Angle : 0.571 9.175 24327 Z= 0.302 Chirality : 0.039 0.146 2859 Planarity : 0.004 0.062 3079 Dihedral : 3.689 20.091 2371 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.10 % Allowed : 18.49 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.18), residues: 2225 helix: 2.37 (0.14), residues: 1427 sheet: 1.66 (0.44), residues: 161 loop : -1.25 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 100 TYR 0.025 0.002 TYR A 323 PHE 0.014 0.001 PHE B 50 TRP 0.013 0.001 TRP D 37 HIS 0.004 0.001 HIS F 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (17981) covalent geometry : angle 0.57057 / 0.30 (24327) hydrogen bonds : bond 0.05261 / 3.41 ( 1166) hydrogen bonds : angle 4.17562 / 2.98 ( 3420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 87 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8789 (ttp80) REVERT: A 286 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8968 (mmtm) REVERT: B 102 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: B 279 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8486 (pp20) REVERT: C 135 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8780 (mmmt) REVERT: C 271 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8779 (pp) REVERT: C 351 MET cc_start: 0.7540 (tpp) cc_final: 0.7125 (tmm) REVERT: D 174 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9033 (mt) REVERT: D 271 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9084 (pp) REVERT: D 282 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8463 (mp) REVERT: F 157 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.8898 (m-30) outliers start: 61 outliers final: 25 residues processed: 144 average time/residue: 0.1393 time to fit residues: 30.8008 Evaluate side-chains 112 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 303 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 158 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.108692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070223 restraints weight = 44010.083| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.34 r_work: 0.2997 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17981 Z= 0.118 Angle : 0.461 8.113 24327 Z= 0.242 Chirality : 0.035 0.136 2859 Planarity : 0.004 0.050 3079 Dihedral : 3.463 18.661 2371 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.39 % Allowed : 18.74 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.19), residues: 2225 helix: 2.69 (0.14), residues: 1439 sheet: 2.00 (0.45), residues: 160 loop : -1.16 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 301 TYR 0.017 0.001 TYR A 323 PHE 0.007 0.001 PHE E 50 TRP 0.010 0.001 TRP D 37 HIS 0.002 0.000 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17981) covalent geometry : angle 0.46103 / 0.24 (24327) hydrogen bonds : bond 0.04076 / 2.65 ( 1166) hydrogen bonds : angle 3.64623 / 2.61 ( 3420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 88 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8834 (t80) cc_final: 0.8598 (t80) REVERT: B 102 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: B 279 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8400 (pp20) REVERT: C 135 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8888 (mmmt) REVERT: C 150 GLU cc_start: 0.8612 (pm20) cc_final: 0.8160 (pm20) REVERT: C 271 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8623 (pp) REVERT: D 174 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8986 (mt) REVERT: E 102 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8628 (pm20) REVERT: E 126 TYR cc_start: 0.8921 (t80) cc_final: 0.8564 (t80) REVERT: E 295 ASN cc_start: 0.8325 (t0) cc_final: 0.8124 (t0) REVERT: G 90 ARG cc_start: 0.8489 (mmt90) cc_final: 0.8283 (mmt90) REVERT: G 183 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6364 (mp0) outliers start: 47 outliers final: 22 residues processed: 127 average time/residue: 0.1387 time to fit residues: 26.8805 Evaluate side-chains 111 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TRP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 172 TRP Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 303 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 222 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 163 optimal weight: 50.0000 chunk 25 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN B 307 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.106918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.068171 restraints weight = 43909.153| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.23 r_work: 0.2944 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17981 Z= 0.208 Angle : 0.507 7.672 24327 Z= 0.265 Chirality : 0.037 0.141 2859 Planarity : 0.004 0.045 3079 Dihedral : 3.531 19.056 2371 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.10 % Allowed : 18.64 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.19), residues: 2225 helix: 2.74 (0.14), residues: 1436 sheet: 1.90 (0.44), residues: 159 loop : -1.17 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 280 TYR 0.020 0.002 TYR A 323 PHE 0.009 0.001 PHE F 269 TRP 0.009 0.001 TRP B 37 HIS 0.003 0.001 HIS F 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (17981) covalent geometry : angle 0.50697 / 0.26 (24327) hydrogen bonds : bond 0.04195 / 2.71 ( 1166) hydrogen bonds : angle 3.65696 / 2.62 ( 3420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 86 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8843 (t80) cc_final: 0.8548 (t80) REVERT: B 102 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: B 279 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8363 (pp20) REVERT: C 271 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8766 (pp) REVERT: D 174 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9022 (mt) REVERT: D 189 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9093 (p) REVERT: D 282 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8488 (mp) REVERT: E 102 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: F 128 MET cc_start: 0.8800 (mmm) cc_final: 0.8574 (mmp) REVERT: G 90 ARG cc_start: 0.8446 (mmt90) cc_final: 0.8219 (mmt90) REVERT: G 226 ARG cc_start: 0.9324 (ttm-80) cc_final: 0.9088 (ttm-80) outliers start: 61 outliers final: 35 residues processed: 137 average time/residue: 0.1316 time to fit residues: 28.2236 Evaluate side-chains 122 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TRP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain G residue 172 TRP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 19 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 219 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 78 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.108167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069568 restraints weight = 43592.759| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.31 r_work: 0.2976 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17981 Z= 0.121 Angle : 0.462 7.067 24327 Z= 0.242 Chirality : 0.035 0.140 2859 Planarity : 0.004 0.040 3079 Dihedral : 3.440 19.219 2371 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 2.84 % Allowed : 19.10 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.19), residues: 2225 helix: 2.87 (0.14), residues: 1439 sheet: 1.98 (0.44), residues: 159 loop : -1.11 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 226 TYR 0.015 0.001 TYR A 323 PHE 0.008 0.001 PHE E 50 TRP 0.037 0.001 TRP D 37 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17981) covalent geometry : angle 0.46171 / 0.24 (24327) hydrogen bonds : bond 0.03777 / 2.45 ( 1166) hydrogen bonds : angle 3.45440 / 2.47 ( 3420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 88 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7074 (p0) REVERT: A 126 TYR cc_start: 0.8838 (t80) cc_final: 0.8596 (t80) REVERT: A 236 ASN cc_start: 0.9202 (m-40) cc_final: 0.8977 (m110) REVERT: A 286 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8305 (mtmm) REVERT: B 102 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: C 271 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8643 (pp) REVERT: D 174 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8999 (mt) REVERT: E 102 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: E 126 TYR cc_start: 0.8981 (t80) cc_final: 0.8671 (t80) REVERT: F 128 MET cc_start: 0.8789 (mmm) cc_final: 0.8536 (mmp) REVERT: G 90 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8271 (mmt90) REVERT: G 226 ARG cc_start: 0.9335 (ttm-80) cc_final: 0.9107 (ttm-80) outliers start: 56 outliers final: 35 residues processed: 135 average time/residue: 0.1409 time to fit residues: 29.1983 Evaluate side-chains 121 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 37 TRP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain G residue 172 TRP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.106410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067550 restraints weight = 43931.724| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.30 r_work: 0.2952 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17981 Z= 0.166 Angle : 0.489 8.330 24327 Z= 0.254 Chirality : 0.036 0.134 2859 Planarity : 0.004 0.040 3079 Dihedral : 3.448 19.049 2371 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 2.84 % Allowed : 19.55 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.19), residues: 2225 helix: 2.89 (0.14), residues: 1438 sheet: 1.92 (0.44), residues: 159 loop : -1.11 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 239 TYR 0.027 0.002 TYR G 169 PHE 0.022 0.001 PHE A 217 TRP 0.028 0.001 TRP D 37 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (17981) covalent geometry : angle 0.48896 / 0.25 (24327) hydrogen bonds : bond 0.03839 / 2.48 ( 1166) hydrogen bonds : angle 3.46323 / 2.48 ( 3420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 84 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8812 (t80) cc_final: 0.8558 (t80) REVERT: B 97 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8551 (ptpp) REVERT: B 102 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: C 271 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8710 (pp) REVERT: D 174 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9041 (mt) REVERT: E 102 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8639 (pm20) REVERT: E 126 TYR cc_start: 0.9026 (t80) cc_final: 0.8735 (t80) REVERT: F 128 MET cc_start: 0.8779 (mmm) cc_final: 0.8578 (mmp) REVERT: G 90 ARG cc_start: 0.8493 (mmt90) cc_final: 0.8269 (mmt90) REVERT: G 226 ARG cc_start: 0.9342 (ttm-80) cc_final: 0.9125 (ttm-80) outliers start: 56 outliers final: 42 residues processed: 130 average time/residue: 0.1306 time to fit residues: 25.9069 Evaluate side-chains 129 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 82 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TRP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain G residue 172 TRP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 167 optimal weight: 0.9980 chunk 121 optimal weight: 0.0870 chunk 89 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 30 optimal weight: 30.0000 chunk 205 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.105177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066734 restraints weight = 44920.276| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.26 r_work: 0.2993 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17981 Z= 0.101 Angle : 0.453 8.640 24327 Z= 0.234 Chirality : 0.035 0.145 2859 Planarity : 0.004 0.040 3079 Dihedral : 3.347 18.872 2371 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 2.34 % Allowed : 19.96 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.19), residues: 2225 helix: 3.05 (0.14), residues: 1437 sheet: 1.99 (0.43), residues: 159 loop : -1.06 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.014 0.001 TYR F 194 PHE 0.008 0.001 PHE E 50 TRP 0.026 0.001 TRP D 37 HIS 0.002 0.000 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (17981) covalent geometry : angle 0.45276 / 0.23 (24327) hydrogen bonds : bond 0.03499 / 2.27 ( 1166) hydrogen bonds : angle 3.28354 / 2.35 ( 3420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 90 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 126 TYR cc_start: 0.8776 (t80) cc_final: 0.8557 (t80) REVERT: A 236 ASN cc_start: 0.9208 (m-40) cc_final: 0.8974 (m110) REVERT: B 102 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: C 271 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8618 (pp) REVERT: D 174 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8979 (mt) REVERT: D 333 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8695 (ttmt) REVERT: E 126 TYR cc_start: 0.8930 (t80) cc_final: 0.8592 (t80) REVERT: F 128 MET cc_start: 0.8785 (mmm) cc_final: 0.8532 (mmp) REVERT: G 90 ARG cc_start: 0.8527 (mmt90) cc_final: 0.8313 (mmt90) REVERT: G 226 ARG cc_start: 0.9337 (ttm-80) cc_final: 0.9127 (ttm-80) outliers start: 46 outliers final: 31 residues processed: 126 average time/residue: 0.1324 time to fit residues: 25.5566 Evaluate side-chains 119 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 37 TRP Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain G residue 172 TRP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 280 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 121 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 187 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.103836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065209 restraints weight = 45095.474| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.34 r_work: 0.3009 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 17981 Z= 0.107 Angle : 0.472 10.428 24327 Z= 0.240 Chirality : 0.035 0.128 2859 Planarity : 0.004 0.040 3079 Dihedral : 3.310 18.756 2371 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.23 % Allowed : 20.31 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.19), residues: 2225 helix: 3.10 (0.14), residues: 1438 sheet: 2.01 (0.43), residues: 159 loop : -1.01 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.023 0.001 TYR G 169 PHE 0.024 0.001 PHE A 217 TRP 0.024 0.001 TRP D 37 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17981) covalent geometry : angle 0.47212 / 0.24 (24327) hydrogen bonds : bond 0.03457 / 2.24 ( 1166) hydrogen bonds : angle 3.24502 / 2.32 ( 3420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8835 (mm) REVERT: B 102 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: C 135 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8843 (mmmt) REVERT: C 271 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8573 (pp) REVERT: D 174 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8984 (mt) REVERT: D 333 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8695 (ttmt) REVERT: E 126 TYR cc_start: 0.8938 (t80) cc_final: 0.8709 (t80) REVERT: E 295 ASN cc_start: 0.8379 (t0) cc_final: 0.8173 (t0) REVERT: F 128 MET cc_start: 0.8769 (mmm) cc_final: 0.8564 (mmp) REVERT: G 226 ARG cc_start: 0.9342 (ttm-80) cc_final: 0.9138 (ttm-80) outliers start: 44 outliers final: 30 residues processed: 121 average time/residue: 0.1408 time to fit residues: 26.1259 Evaluate side-chains 116 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 172 TRP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 136 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 134 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.105064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066653 restraints weight = 44903.233| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.34 r_work: 0.2996 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17981 Z= 0.099 Angle : 0.467 9.944 24327 Z= 0.238 Chirality : 0.035 0.232 2859 Planarity : 0.004 0.039 3079 Dihedral : 3.271 18.168 2371 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.13 % Allowed : 20.47 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.19), residues: 2225 helix: 3.15 (0.14), residues: 1438 sheet: 2.06 (0.43), residues: 159 loop : -0.99 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.018 0.001 TYR A 126 PHE 0.008 0.001 PHE E 50 TRP 0.023 0.001 TRP D 37 HIS 0.002 0.000 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (17981) covalent geometry : angle 0.46651 / 0.24 (24327) hydrogen bonds : bond 0.03336 / 2.16 ( 1166) hydrogen bonds : angle 3.18589 / 2.28 ( 3420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8845 (mm) REVERT: A 236 ASN cc_start: 0.9212 (m-40) cc_final: 0.9008 (m110) REVERT: B 102 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: C 271 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8526 (pp) REVERT: D 174 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9002 (mt) REVERT: D 333 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8647 (ttmt) REVERT: E 126 TYR cc_start: 0.8825 (t80) cc_final: 0.8597 (t80) REVERT: E 128 MET cc_start: 0.8935 (mmt) cc_final: 0.8719 (mmt) REVERT: F 128 MET cc_start: 0.8772 (mmm) cc_final: 0.8507 (mmp) REVERT: G 226 ARG cc_start: 0.9308 (ttm-80) cc_final: 0.9093 (ttm-80) outliers start: 42 outliers final: 31 residues processed: 119 average time/residue: 0.1261 time to fit residues: 23.7391 Evaluate side-chains 116 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 172 TRP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 193 optimal weight: 0.0770 chunk 184 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 152 optimal weight: 0.0010 chunk 168 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN E 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.102909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064698 restraints weight = 45066.106| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.28 r_work: 0.2994 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17981 Z= 0.123 Angle : 0.481 9.864 24327 Z= 0.244 Chirality : 0.036 0.220 2859 Planarity : 0.004 0.038 3079 Dihedral : 3.280 18.107 2371 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.98 % Allowed : 20.67 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.19), residues: 2225 helix: 3.16 (0.14), residues: 1434 sheet: 2.05 (0.43), residues: 159 loop : -0.97 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.024 0.001 TYR G 169 PHE 0.024 0.001 PHE A 217 TRP 0.022 0.001 TRP D 37 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (17981) covalent geometry : angle 0.48084 / 0.24 (24327) hydrogen bonds : bond 0.03432 / 2.22 ( 1166) hydrogen bonds : angle 3.20725 / 2.29 ( 3420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 83 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6878 (p0) REVERT: A 56 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8852 (mm) REVERT: A 236 ASN cc_start: 0.9212 (m-40) cc_final: 0.9008 (m110) REVERT: B 102 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: C 271 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8610 (pp) REVERT: D 174 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9005 (mt) REVERT: F 128 MET cc_start: 0.8780 (mmm) cc_final: 0.8530 (mmp) REVERT: G 226 ARG cc_start: 0.9332 (ttm-80) cc_final: 0.9123 (ttm-80) outliers start: 39 outliers final: 29 residues processed: 117 average time/residue: 0.1320 time to fit residues: 24.0793 Evaluate side-chains 113 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 37 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 172 TRP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 163 optimal weight: 50.0000 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 99 optimal weight: 10.0000 chunk 22 optimal weight: 0.0980 chunk 145 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.104639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066025 restraints weight = 45185.125| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.30 r_work: 0.2987 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 17981 Z= 0.148 Angle : 0.697 59.198 24327 Z= 0.402 Chirality : 0.039 0.827 2859 Planarity : 0.004 0.038 3079 Dihedral : 3.298 19.113 2371 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.98 % Allowed : 20.47 % Favored : 77.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.19), residues: 2225 helix: 3.15 (0.14), residues: 1434 sheet: 2.04 (0.43), residues: 159 loop : -0.97 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 239 TYR 0.015 0.001 TYR F 194 PHE 0.013 0.001 PHE A 217 TRP 0.022 0.001 TRP D 37 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (17981) covalent geometry : angle 0.69739 / 0.40 (24327) hydrogen bonds : bond 0.03422 / 2.22 ( 1166) hydrogen bonds : angle 3.20660 / 2.29 ( 3420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.58 seconds wall clock time: 82 minutes 56.19 seconds (4976.19 seconds total)