Starting phenix.real_space_refine on Fri Mar 6 04:43:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ock_12809/03_2026/7ock_12809.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ock_12809/03_2026/7ock_12809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ock_12809/03_2026/7ock_12809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ock_12809/03_2026/7ock_12809.map" model { file = "/net/cci-nas-00/data/ceres_data/7ock_12809/03_2026/7ock_12809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ock_12809/03_2026/7ock_12809.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 136 5.16 5 C 17822 2.51 5 N 4884 2.21 5 O 5434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 217 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28276 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "C" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "D" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "E" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "F" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "G" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "H" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "I" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "L" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1194 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 6, 'TRANS': 145} Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1186 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "K" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1164 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Chain: "J" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1174 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 1 Time building chain proxies: 6.28, per 1000 atoms: 0.22 Number of scatterers: 28276 At special positions: 0 Unit cell: (105.6, 124.3, 261.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 5434 8.00 N 4884 7.00 C 17822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 56 " - pdb=" SG CYS L 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS K 56 " - pdb=" SG CYS K 139 " distance=2.04 Simple disulfide: pdb=" SG CYS J 56 " - pdb=" SG CYS J 139 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6708 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 44 sheets defined 37.9% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'B' and resid 14 through 34 Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.768A pdb=" N ILE B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.576A pdb=" N THR B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.995A pdb=" N MET B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.753A pdb=" N ASP B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 288 removed outlier: 3.856A pdb=" N SER B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.839A pdb=" N ALA B 356 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.630A pdb=" N ALA B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 34 Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.763A pdb=" N ILE C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 removed outlier: 3.680A pdb=" N VAL C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.636A pdb=" N GLY C 155 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.528A pdb=" N ILE C 206 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.601A pdb=" N THR C 250 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 289 removed outlier: 3.563A pdb=" N SER C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 352 through 356 removed outlier: 4.090A pdb=" N ALA C 356 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 371 through 380 removed outlier: 4.269A pdb=" N LEU C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 34 Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.245A pdb=" N GLN D 104 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 154 removed outlier: 3.629A pdb=" N THR D 139 " --> pdb=" O PRO D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 233 through 238 removed outlier: 4.098A pdb=" N GLY D 237 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 238' Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 269 through 288 removed outlier: 3.889A pdb=" N SER D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'D' and resid 336 through 345 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.614A pdb=" N THR D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 371 No H-bonds generated for 'chain 'D' and resid 370 through 371' Processing helix chain 'D' and resid 372 through 380 removed outlier: 3.700A pdb=" N ALA D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 34 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.591A pdb=" N ILE E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 135 through 155 Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 206 through 211 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.807A pdb=" N MET E 236 " --> pdb=" O GLY E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.750A pdb=" N THR E 250 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 288 removed outlier: 3.791A pdb=" N SER E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 Processing helix chain 'E' and resid 336 through 345 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.543A pdb=" N THR E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 370 through 380 removed outlier: 4.132A pdb=" N GLN E 374 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU E 375 " --> pdb=" O ASP E 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 34 Processing helix chain 'F' and resid 63 through 76 removed outlier: 3.627A pdb=" N ILE F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 83 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'F' and resid 135 through 155 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 206 through 211 Processing helix chain 'F' and resid 245 through 250 removed outlier: 4.313A pdb=" N ASP F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 250' Processing helix chain 'F' and resid 269 through 289 removed outlier: 3.610A pdb=" N SER F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 333 removed outlier: 3.518A pdb=" N PHE F 333 " --> pdb=" O VAL F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 345 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.976A pdb=" N THR F 354 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 369 Processing helix chain 'F' and resid 370 through 371 No H-bonds generated for 'chain 'F' and resid 370 through 371' Processing helix chain 'F' and resid 372 through 380 Processing helix chain 'G' and resid 14 through 34 Processing helix chain 'G' and resid 63 through 76 removed outlier: 3.590A pdb=" N ILE G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 83 Processing helix chain 'G' and resid 99 through 108 removed outlier: 4.090A pdb=" N ASN G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 154 removed outlier: 3.850A pdb=" N THR G 139 " --> pdb=" O PRO G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 Processing helix chain 'G' and resid 206 through 211 Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 245 through 251 Processing helix chain 'G' and resid 269 through 288 removed outlier: 3.939A pdb=" N SER G 273 " --> pdb=" O LYS G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 336 through 345 Processing helix chain 'G' and resid 371 through 381 removed outlier: 4.301A pdb=" N LEU G 375 " --> pdb=" O ASP G 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 381 " --> pdb=" O ARG G 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 34 Processing helix chain 'H' and resid 63 through 76 Processing helix chain 'H' and resid 80 through 83 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 135 through 154 Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 206 through 211 Processing helix chain 'H' and resid 233 through 238 removed outlier: 3.791A pdb=" N GLY H 237 " --> pdb=" O GLY H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 250 Processing helix chain 'H' and resid 269 through 288 Processing helix chain 'H' and resid 321 through 333 Processing helix chain 'H' and resid 336 through 345 Processing helix chain 'H' and resid 350 through 356 removed outlier: 4.258A pdb=" N ALA H 356 " --> pdb=" O LYS H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 380 Processing helix chain 'I' and resid 14 through 34 Processing helix chain 'I' and resid 63 through 76 removed outlier: 3.748A pdb=" N ILE I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 106 Processing helix chain 'I' and resid 135 through 154 Processing helix chain 'I' and resid 194 through 206 Processing helix chain 'I' and resid 206 through 211 Processing helix chain 'I' and resid 245 through 250 Processing helix chain 'I' and resid 269 through 288 removed outlier: 3.743A pdb=" N SER I 273 " --> pdb=" O LYS I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 333 Processing helix chain 'I' and resid 336 through 345 Processing helix chain 'I' and resid 350 through 355 Processing helix chain 'I' and resid 365 through 369 removed outlier: 3.517A pdb=" N GLU I 368 " --> pdb=" O PHE I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 380 Processing helix chain 'L' and resid 23 through 41 removed outlier: 3.520A pdb=" N MET L 28 " --> pdb=" O ASP L 24 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 79 through 92 Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.959A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'K' and resid 24 through 41 Processing helix chain 'K' and resid 79 through 92 Processing helix chain 'J' and resid 23 through 41 Processing helix chain 'J' and resid 41 through 46 Processing helix chain 'J' and resid 79 through 92 Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 10 removed outlier: 5.393A pdb=" N ARG B 161 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N HIS B 189 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP B 163 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 187 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS B 165 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 185 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN B 167 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 183 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 169 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 179 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP B 173 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 45 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 45 removed outlier: 7.008A pdb=" N GLY B 96 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY B 54 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN B 98 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 56 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 127 removed outlier: 3.566A pdb=" N SER B 309 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 10 removed outlier: 5.849A pdb=" N ARG C 161 " --> pdb=" O HIS C 189 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS C 189 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP C 163 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR C 187 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS C 165 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU C 185 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN C 167 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 183 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR C 169 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 179 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP C 173 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 45 Processing sheet with id=AA8, first strand: chain 'C' and resid 38 through 45 removed outlier: 7.326A pdb=" N GLY C 96 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY C 54 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLN C 98 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 56 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'C' and resid 120 through 127 removed outlier: 3.779A pdb=" N SER C 309 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 10 removed outlier: 4.143A pdb=" N GLN D 188 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP D 163 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER D 186 " --> pdb=" O ASP D 163 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS D 165 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 184 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN D 167 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA D 182 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR D 169 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE D 180 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN D 171 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 38 through 45 removed outlier: 6.745A pdb=" N VAL D 50 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA D 94 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL D 52 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY D 96 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY D 54 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 78 through 79 Processing sheet with id=AB5, first strand: chain 'D' and resid 120 through 127 Processing sheet with id=AB6, first strand: chain 'E' and resid 3 through 10 removed outlier: 3.799A pdb=" N GLN E 188 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP E 163 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER E 186 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS E 165 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL E 184 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLN E 167 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA E 182 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR E 169 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE E 180 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN E 171 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 90 through 98 removed outlier: 6.655A pdb=" N VAL E 50 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA E 94 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL E 52 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY E 96 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY E 54 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN E 98 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE E 56 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 120 through 127 Processing sheet with id=AB9, first strand: chain 'F' and resid 2 through 10 removed outlier: 5.997A pdb=" N ARG F 161 " --> pdb=" O HIS F 189 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS F 189 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP F 163 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR F 187 " --> pdb=" O ASP F 163 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS F 165 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU F 185 " --> pdb=" O LYS F 165 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN F 167 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL F 183 " --> pdb=" O GLN F 167 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR F 169 " --> pdb=" O ASP F 181 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY F 179 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP F 173 " --> pdb=" O ILE F 177 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 90 through 94 removed outlier: 4.059A pdb=" N GLY F 54 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.734A pdb=" N HIS F 79 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 84 " --> pdb=" O HIS F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 120 through 127 Processing sheet with id=AC4, first strand: chain 'G' and resid 2 through 10 removed outlier: 7.034A pdb=" N ASP G 163 " --> pdb=" O SER G 186 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER G 186 " --> pdb=" O ASP G 163 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 165 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL G 184 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN G 167 " --> pdb=" O ALA G 182 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA G 182 " --> pdb=" O GLN G 167 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 169 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE G 180 " --> pdb=" O THR G 169 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN G 171 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LYS G 221 " --> pdb=" O GLY G 179 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP G 181 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N PHE G 223 " --> pdb=" O ASP G 181 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL G 183 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 90 through 93 Processing sheet with id=AC6, first strand: chain 'G' and resid 90 through 93 Processing sheet with id=AC7, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AC8, first strand: chain 'G' and resid 120 through 127 Processing sheet with id=AC9, first strand: chain 'H' and resid 5 through 10 removed outlier: 4.198A pdb=" N GLN H 188 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP H 163 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER H 186 " --> pdb=" O ASP H 163 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS H 165 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 184 " --> pdb=" O LYS H 165 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN H 167 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA H 182 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR H 169 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE H 180 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN H 171 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 178 " --> pdb=" O GLN H 171 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 90 through 96 removed outlier: 6.285A pdb=" N VAL H 50 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA H 94 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL H 52 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY H 96 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY H 54 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 78 through 79 Processing sheet with id=AD3, first strand: chain 'H' and resid 120 through 126 Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 10 removed outlier: 5.112A pdb=" N ASP I 163 " --> pdb=" O GLN I 188 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN I 171 " --> pdb=" O ILE I 180 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE I 180 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP I 173 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 90 through 95 Processing sheet with id=AD6, first strand: chain 'I' and resid 78 through 79 Processing sheet with id=AD7, first strand: chain 'I' and resid 120 through 127 Processing sheet with id=AD8, first strand: chain 'L' and resid 49 through 50 removed outlier: 3.965A pdb=" N LEU L 98 " --> pdb=" O VAL L 15 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 66 through 69 removed outlier: 3.501A pdb=" N ILE L 142 " --> pdb=" O PHE L 145 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.613A pdb=" N VAL A 71 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 16 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 98 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 66 through 69 removed outlier: 3.905A pdb=" N ILE A 142 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 47 through 50 Processing sheet with id=AE4, first strand: chain 'K' and resid 47 through 50 Processing sheet with id=AE5, first strand: chain 'K' and resid 126 through 129 removed outlier: 5.151A pdb=" N ARG K 148 " --> pdb=" O GLN K 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 47 through 48 removed outlier: 3.896A pdb=" N LEU J 98 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 66 through 69 Processing sheet with id=AE8, first strand: chain 'J' and resid 126 through 129 removed outlier: 4.901A pdb=" N PHE J 127 " --> pdb=" O GLN J 150 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN J 150 " --> pdb=" O PHE J 127 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3645 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: 5.71 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9517 1.34 - 1.46: 5422 1.46 - 1.57: 13694 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 28849 Sorted by residual: bond pdb=" C ILE G 210 " pdb=" N LEU G 211 " ideal model delta sigma weight residual 1.331 1.285 0.046 2.07e-02 2.33e+03 4.86e+00 bond pdb=" CB PHE B 84 " pdb=" CG PHE B 84 " ideal model delta sigma weight residual 1.502 1.453 0.049 2.30e-02 1.89e+03 4.46e+00 bond pdb=" CA HIS C 189 " pdb=" CB HIS C 189 " ideal model delta sigma weight residual 1.535 1.493 0.043 2.09e-02 2.29e+03 4.15e+00 bond pdb=" CA PHE D 360 " pdb=" CB PHE D 360 " ideal model delta sigma weight residual 1.534 1.504 0.030 1.57e-02 4.06e+03 3.65e+00 bond pdb=" CB PHE A 3 " pdb=" CG PHE A 3 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.60e+00 ... (remaining 28844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 38419 2.61 - 5.22: 627 5.22 - 7.83: 43 7.83 - 10.44: 8 10.44 - 13.05: 2 Bond angle restraints: 39099 Sorted by residual: angle pdb=" N VAL H 132 " pdb=" CA VAL H 132 " pdb=" C VAL H 132 " ideal model delta sigma weight residual 112.83 106.65 6.18 9.90e-01 1.02e+00 3.90e+01 angle pdb=" CA CYS L 139 " pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " ideal model delta sigma weight residual 114.40 127.45 -13.05 2.30e+00 1.89e-01 3.22e+01 angle pdb=" N VAL I 132 " pdb=" CA VAL I 132 " pdb=" C VAL I 132 " ideal model delta sigma weight residual 111.91 107.25 4.66 8.90e-01 1.26e+00 2.75e+01 angle pdb=" CA CYS K 56 " pdb=" CB CYS K 56 " pdb=" SG CYS K 56 " ideal model delta sigma weight residual 114.40 124.54 -10.14 2.30e+00 1.89e-01 1.94e+01 angle pdb=" CA CYS L 56 " pdb=" CB CYS L 56 " pdb=" SG CYS L 56 " ideal model delta sigma weight residual 114.40 124.36 -9.96 2.30e+00 1.89e-01 1.88e+01 ... (remaining 39094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 15535 18.06 - 36.12: 1467 36.12 - 54.18: 236 54.18 - 72.24: 48 72.24 - 90.30: 42 Dihedral angle restraints: 17328 sinusoidal: 6848 harmonic: 10480 Sorted by residual: dihedral pdb=" CB CYS A 56 " pdb=" SG CYS A 56 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -0.06 -85.94 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS J 56 " pdb=" SG CYS J 56 " pdb=" SG CYS J 139 " pdb=" CB CYS J 139 " ideal model delta sinusoidal sigma weight residual -86.00 -6.41 -79.59 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CA CYS L 23 " pdb=" C CYS L 23 " pdb=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta harmonic sigma weight residual -180.00 -147.83 -32.17 0 5.00e+00 4.00e-02 4.14e+01 ... (remaining 17325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3056 0.042 - 0.085: 975 0.085 - 0.127: 290 0.127 - 0.169: 30 0.169 - 0.211: 8 Chirality restraints: 4359 Sorted by residual: chirality pdb=" CB ILE L 61 " pdb=" CA ILE L 61 " pdb=" CG1 ILE L 61 " pdb=" CG2 ILE L 61 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLU K 6 " pdb=" N GLU K 6 " pdb=" C GLU K 6 " pdb=" CB GLU K 6 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" C PRO C 162 " pdb=" CB PRO C 162 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 4356 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 123 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO L 124 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 124 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 124 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 130 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO J 131 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO J 131 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO J 131 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET G 134 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO G 135 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 135 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 135 " -0.031 5.00e-02 4.00e+02 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 675 2.57 - 3.15: 28772 3.15 - 3.74: 50507 3.74 - 4.32: 69128 4.32 - 4.90: 105435 Nonbonded interactions: 254517 Sorted by model distance: nonbonded pdb=" O TYR I 125 " pdb=" OH TYR I 251 " model vdw 1.988 3.040 nonbonded pdb=" OD1 ASP B 194 " pdb=" OG SER B 197 " model vdw 1.998 3.040 nonbonded pdb=" O GLN A 128 " pdb=" NH1 ARG A 147 " model vdw 2.018 3.120 nonbonded pdb=" OD1 ASP F 194 " pdb=" OG SER F 197 " model vdw 2.026 3.040 nonbonded pdb=" OG SER B 299 " pdb=" OG1 THR B 308 " model vdw 2.044 3.040 ... (remaining 254512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 59 or resid 65 through 153)) selection = (chain 'J' and (resid 3 through 59 or resid 65 through 153)) selection = (chain 'K' and resid 3 through 153) selection = (chain 'L' and (resid 3 through 59 or resid 65 through 153)) } ncs_group { reference = (chain 'B' and resid 1 through 383) selection = (chain 'C' and resid 1 through 383) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 1 through 383) selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.930 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4191 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 : 0.008 0.058 28853 Z= 0.383 Angle : 0.865 13.048 39107 Z= 0.504 Chirality : 0.045 0.211 4359 Planarity : 0.005 0.064 5118 Dihedral : 14.977 90.301 10608 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 36.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 0.20 % Allowed : 9.45 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.12), residues: 3638 helix: -2.36 (0.12), residues: 1148 sheet: -0.78 (0.17), residues: 798 loop : -2.16 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 279 TYR 0.027 0.003 TYR K 100 PHE 0.032 0.002 PHE K 140 TRP 0.016 0.002 TRP G 159 HIS 0.011 0.003 HIS G 364 Details of bonding type rmsd covalent geometry : bond 0.00767 (28849) covalent geometry : angle 0.86268 (39099) SS BOND : bond 0.00902 ( 4) SS BOND : angle 4.51196 ( 8) hydrogen bonds : bond 0.16871 ( 1297) hydrogen bonds : angle 7.64371 ( 3645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 498 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 PRO cc_start: 0.3759 (Cg_exo) cc_final: 0.3160 (Cg_endo) REVERT: B 343 MET cc_start: 0.3541 (ttp) cc_final: 0.3271 (mtp) REVERT: E 185 LEU cc_start: 0.7472 (tp) cc_final: 0.6960 (mp) REVERT: G 185 LEU cc_start: 0.7767 (tt) cc_final: 0.7528 (mt) REVERT: I 215 TRP cc_start: 0.7380 (m-10) cc_final: 0.7026 (m-10) REVERT: I 345 ASP cc_start: 0.7996 (t0) cc_final: 0.7757 (t0) REVERT: L 28 MET cc_start: 0.9058 (mmm) cc_final: 0.8202 (tpp) REVERT: L 53 LEU cc_start: 0.5538 (tp) cc_final: 0.4845 (tp) REVERT: L 56 CYS cc_start: 0.0349 (OUTLIER) cc_final: -0.0157 (m) REVERT: L 83 ASN cc_start: 0.9242 (t0) cc_final: 0.9036 (t0) REVERT: L 87 LEU cc_start: 0.8466 (mt) cc_final: 0.8006 (mt) REVERT: L 142 ILE cc_start: 0.5470 (tt) cc_final: 0.4603 (tt) REVERT: K 12 TYR cc_start: 0.1790 (m-80) cc_final: 0.0579 (m-80) REVERT: K 13 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.6509 (m) REVERT: K 98 LEU cc_start: 0.6676 (mp) cc_final: 0.5755 (tt) REVERT: K 127 PHE cc_start: 0.5151 (t80) cc_final: 0.4344 (t80) REVERT: J 109 LEU cc_start: 0.6376 (pt) cc_final: 0.5529 (pt) outliers start: 6 outliers final: 2 residues processed: 504 average time/residue: 0.2069 time to fit residues: 157.4267 Evaluate side-chains 280 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 276 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain J residue 139 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 195 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS B 297 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS C 21 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 119 GLN E 14 HIS ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 195 GLN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN F 87 ASN F 104 GLN F 119 GLN ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 297 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 HIS F 359 HIS G 14 HIS G 70 ASN G 79 HIS G 146 GLN G 171 GLN G 195 GLN G 297 GLN H 3 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS H 87 ASN H 103 ASN H 104 GLN H 114 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN H 167 GLN H 225 ASN H 257 HIS ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 HIS I 33 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 ASN ** I 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 GLN ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 152 GLN K 103 GLN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.059476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.047382 restraints weight = 210770.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.048656 restraints weight = 141376.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.049501 restraints weight = 100132.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.050214 restraints weight = 75946.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.050803 restraints weight = 61574.549| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4757 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28853 Z= 0.198 Angle : 0.789 11.225 39107 Z= 0.412 Chirality : 0.048 0.212 4359 Planarity : 0.006 0.102 5118 Dihedral : 5.939 59.705 3964 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 24.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 2.70 % Allowed : 15.85 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.22 (0.14), residues: 3638 helix: -0.38 (0.14), residues: 1149 sheet: -0.08 (0.18), residues: 750 loop : -1.40 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 147 TYR 0.031 0.003 TYR F 280 PHE 0.023 0.003 PHE I 230 TRP 0.033 0.003 TRP B 215 HIS 0.018 0.002 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00418 (28849) covalent geometry : angle 0.78790 (39099) SS BOND : bond 0.00717 ( 4) SS BOND : angle 2.50551 ( 8) hydrogen bonds : bond 0.04667 ( 1297) hydrogen bonds : angle 6.40837 ( 3645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 321 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.3072 (ttp) cc_final: 0.2858 (mtp) REVERT: D 272 ARG cc_start: 0.0955 (OUTLIER) cc_final: -0.0230 (ttp80) REVERT: D 365 PHE cc_start: 0.0428 (m-80) cc_final: 0.0220 (m-80) REVERT: E 353 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.4851 (pt0) REVERT: F 184 VAL cc_start: 0.6495 (OUTLIER) cc_final: 0.6261 (p) REVERT: F 360 PHE cc_start: 0.6064 (m-80) cc_final: 0.5845 (m-10) REVERT: F 367 TRP cc_start: 0.6959 (p90) cc_final: 0.6193 (p90) REVERT: G 30 ILE cc_start: 0.3952 (OUTLIER) cc_final: 0.3605 (tp) REVERT: G 32 GLU cc_start: 0.8680 (tt0) cc_final: 0.8451 (mt-10) REVERT: G 46 LYS cc_start: 0.7559 (tppt) cc_final: 0.6733 (tttm) REVERT: G 185 LEU cc_start: 0.8102 (tt) cc_final: 0.7782 (mt) REVERT: H 173 ASP cc_start: 0.8970 (m-30) cc_final: 0.8653 (p0) REVERT: I 82 MET cc_start: 0.1298 (mmt) cc_final: 0.0890 (mmm) REVERT: I 345 ASP cc_start: 0.8059 (t0) cc_final: 0.7625 (t0) REVERT: L 28 MET cc_start: 0.8781 (mmm) cc_final: 0.7928 (tpp) REVERT: L 83 ASN cc_start: 0.9184 (t0) cc_final: 0.8896 (t0) REVERT: L 143 ASP cc_start: 0.8476 (t70) cc_final: 0.8094 (t70) REVERT: A 28 MET cc_start: 0.8552 (tpp) cc_final: 0.8325 (tpp) outliers start: 81 outliers final: 42 residues processed: 386 average time/residue: 0.1910 time to fit residues: 115.6181 Evaluate side-chains 294 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 293 ARG Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 139 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 169 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 276 optimal weight: 40.0000 chunk 37 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 142 HIS B 167 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 359 HIS ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN F 297 GLN F 359 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN H 148 GLN H 171 GLN H 297 GLN H 374 GLN I 3 HIS ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 HIS ** I 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN L 31 HIS ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN K 150 GLN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.055430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.044379 restraints weight = 229490.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.045447 restraints weight = 156895.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.046021 restraints weight = 115453.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.046651 restraints weight = 90769.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.046970 restraints weight = 75550.750| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 28853 Z= 0.373 Angle : 1.083 18.612 39107 Z= 0.569 Chirality : 0.058 0.446 4359 Planarity : 0.009 0.126 5118 Dihedral : 7.072 56.479 3962 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 46.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.71 % Favored : 93.18 % Rotamer: Outliers : 6.51 % Allowed : 17.42 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.01 (0.13), residues: 3638 helix: -1.09 (0.13), residues: 1174 sheet: -0.72 (0.18), residues: 757 loop : -1.73 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG B 161 TYR 0.042 0.004 TYR C 44 PHE 0.039 0.004 PHE I 84 TRP 0.031 0.004 TRP L 92 HIS 0.075 0.004 HIS F 359 Details of bonding type rmsd covalent geometry : bond 0.00770 (28849) covalent geometry : angle 1.08220 (39099) SS BOND : bond 0.00409 ( 4) SS BOND : angle 2.30815 ( 8) hydrogen bonds : bond 0.06221 ( 1297) hydrogen bonds : angle 7.53486 ( 3645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 301 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.6263 (mp) REVERT: C 5 PHE cc_start: 0.5860 (t80) cc_final: 0.5495 (t80) REVERT: C 129 GLU cc_start: 0.6004 (tt0) cc_final: 0.5739 (pt0) REVERT: C 333 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7468 (t80) REVERT: C 343 MET cc_start: 0.3799 (OUTLIER) cc_final: 0.3379 (ttt) REVERT: D 92 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6083 (mm) REVERT: D 122 MET cc_start: 0.4880 (mmt) cc_final: 0.4620 (mtt) REVERT: D 246 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7219 (mp) REVERT: E 122 MET cc_start: 0.1930 (mtt) cc_final: 0.1573 (mtt) REVERT: E 353 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5844 (pt0) REVERT: F 46 LYS cc_start: 0.7254 (tppt) cc_final: 0.6439 (tmtt) REVERT: F 62 VAL cc_start: 0.2719 (OUTLIER) cc_final: 0.2072 (m) REVERT: F 224 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7276 (pt) REVERT: F 330 ARG cc_start: 0.6488 (mtm110) cc_final: 0.6174 (mmt90) REVERT: G 32 GLU cc_start: 0.8887 (tt0) cc_final: 0.8619 (mt-10) REVERT: G 46 LYS cc_start: 0.8124 (tppt) cc_final: 0.6991 (tttm) REVERT: G 185 LEU cc_start: 0.8667 (tt) cc_final: 0.8247 (mp) REVERT: G 203 MET cc_start: 0.4287 (tpt) cc_final: 0.3975 (mtp) REVERT: G 293 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7661 (ptp90) REVERT: H 173 ASP cc_start: 0.9044 (m-30) cc_final: 0.8725 (p0) REVERT: I 49 MET cc_start: 0.6551 (tmm) cc_final: 0.6223 (tmm) REVERT: I 215 TRP cc_start: 0.8387 (m-10) cc_final: 0.8008 (m-10) REVERT: I 254 MET cc_start: 0.6225 (tpt) cc_final: 0.4982 (tmm) REVERT: I 262 PHE cc_start: 0.5668 (m-80) cc_final: 0.5249 (m-80) REVERT: L 28 MET cc_start: 0.8778 (mmm) cc_final: 0.8055 (tpp) REVERT: L 101 LYS cc_start: 0.7635 (mttt) cc_final: 0.7363 (ttpt) REVERT: L 139 CYS cc_start: 0.1799 (OUTLIER) cc_final: 0.0559 (m) REVERT: L 140 PHE cc_start: 0.7539 (m-10) cc_final: 0.7129 (m-10) REVERT: L 145 PHE cc_start: 0.7547 (m-80) cc_final: 0.7125 (m-80) REVERT: L 147 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8219 (ptt90) REVERT: A 14 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6047 (pt) REVERT: K 12 TYR cc_start: 0.1798 (OUTLIER) cc_final: 0.0030 (m-80) REVERT: K 13 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8290 (t) REVERT: K 78 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7932 (mmtt) REVERT: J 34 MET cc_start: 0.6508 (mtt) cc_final: 0.4148 (mtt) REVERT: J 53 LEU cc_start: 0.8440 (tp) cc_final: 0.7975 (tp) REVERT: J 109 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6647 (pp) outliers start: 195 outliers final: 79 residues processed: 462 average time/residue: 0.1762 time to fit residues: 130.7190 Evaluate side-chains 328 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 234 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain C residue 333 PHE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 378 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 293 ARG Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain K residue 12 TYR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 18 PHE Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 122 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 140 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 284 optimal weight: 40.0000 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 256 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 279 optimal weight: 0.5980 chunk 199 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 ASN I 114 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 GLN ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 HIS ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.056665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.044849 restraints weight = 217005.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.046151 restraints weight = 146830.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.047033 restraints weight = 100045.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.047427 restraints weight = 78349.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.047758 restraints weight = 64787.481| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 28853 Z= 0.163 Angle : 0.788 14.710 39107 Z= 0.401 Chirality : 0.047 0.182 4359 Planarity : 0.006 0.064 5118 Dihedral : 5.988 34.070 3961 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 3.70 % Allowed : 21.33 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.30 (0.13), residues: 3638 helix: -0.25 (0.14), residues: 1171 sheet: -0.48 (0.18), residues: 767 loop : -1.42 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 39 TYR 0.038 0.003 TYR E 357 PHE 0.026 0.002 PHE I 84 TRP 0.020 0.002 TRP B 215 HIS 0.013 0.002 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00367 (28849) covalent geometry : angle 0.78676 (39099) SS BOND : bond 0.00451 ( 4) SS BOND : angle 3.12833 ( 8) hydrogen bonds : bond 0.04401 ( 1297) hydrogen bonds : angle 6.43556 ( 3645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 273 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ASN cc_start: 0.7139 (t0) cc_final: 0.6899 (t0) REVERT: B 203 MET cc_start: 0.8329 (mmm) cc_final: 0.7929 (mmm) REVERT: B 343 MET cc_start: 0.3515 (ttm) cc_final: 0.2782 (mtp) REVERT: C 129 GLU cc_start: 0.5496 (tt0) cc_final: 0.5145 (pt0) REVERT: C 343 MET cc_start: 0.3773 (OUTLIER) cc_final: 0.3082 (ttt) REVERT: D 246 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6570 (mp) REVERT: D 272 ARG cc_start: 0.1788 (OUTLIER) cc_final: 0.1314 (ttp80) REVERT: E 353 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6577 (pt0) REVERT: F 51 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8556 (mm) REVERT: F 184 VAL cc_start: 0.7172 (OUTLIER) cc_final: 0.6872 (p) REVERT: F 330 ARG cc_start: 0.6562 (mtm110) cc_final: 0.6330 (mmt90) REVERT: G 30 ILE cc_start: 0.4833 (OUTLIER) cc_final: 0.4546 (tp) REVERT: G 44 TYR cc_start: 0.7713 (t80) cc_final: 0.7428 (m-80) REVERT: G 46 LYS cc_start: 0.8084 (tppt) cc_final: 0.7027 (tttp) REVERT: G 131 ASP cc_start: 0.7686 (m-30) cc_final: 0.7405 (p0) REVERT: G 203 MET cc_start: 0.4139 (tpt) cc_final: 0.3886 (mtp) REVERT: G 343 MET cc_start: 0.6015 (ptt) cc_final: 0.5543 (ptt) REVERT: H 14 HIS cc_start: 0.7798 (m-70) cc_final: 0.7569 (m-70) REVERT: H 49 MET cc_start: 0.7714 (ppp) cc_final: 0.7489 (ppp) REVERT: H 173 ASP cc_start: 0.8998 (m-30) cc_final: 0.8607 (p0) REVERT: I 215 TRP cc_start: 0.8212 (m-10) cc_final: 0.7801 (m-10) REVERT: I 254 MET cc_start: 0.6150 (tpt) cc_final: 0.5026 (tmm) REVERT: L 28 MET cc_start: 0.8825 (mmm) cc_final: 0.8003 (tpp) REVERT: L 34 MET cc_start: 0.6598 (mtt) cc_final: 0.6086 (mtt) REVERT: L 101 LYS cc_start: 0.7452 (mttt) cc_final: 0.7197 (ttpt) REVERT: A 12 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5476 (t80) REVERT: K 13 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.6572 (t) REVERT: K 33 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.7339 (m90) REVERT: K 78 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7888 (mmtt) REVERT: J 12 TYR cc_start: 0.5412 (m-80) cc_final: 0.4833 (m-80) REVERT: J 109 LEU cc_start: 0.6998 (pt) cc_final: 0.6630 (pp) REVERT: J 149 TRP cc_start: 0.3633 (OUTLIER) cc_final: 0.2884 (p-90) outliers start: 111 outliers final: 58 residues processed: 361 average time/residue: 0.1757 time to fit residues: 102.9333 Evaluate side-chains 296 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 227 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 22 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 270 optimal weight: 40.0000 chunk 280 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 284 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN B 374 GLN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 79 HIS C 167 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN G 225 ASN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS L 31 HIS L 137 GLN ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.054843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.043412 restraints weight = 231771.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.044581 restraints weight = 157088.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.045324 restraints weight = 112807.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.045889 restraints weight = 85778.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.046509 restraints weight = 71275.583| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.8030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 28853 Z= 0.260 Angle : 0.889 16.836 39107 Z= 0.464 Chirality : 0.051 0.250 4359 Planarity : 0.007 0.074 5118 Dihedral : 6.452 36.621 3961 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 38.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.51 % Favored : 93.38 % Rotamer: Outliers : 5.14 % Allowed : 22.10 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.69 (0.13), residues: 3638 helix: -0.51 (0.14), residues: 1171 sheet: -0.88 (0.18), residues: 767 loop : -1.62 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 256 TYR 0.029 0.004 TYR G 338 PHE 0.038 0.003 PHE C 84 TRP 0.043 0.003 TRP G 367 HIS 0.016 0.002 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00572 (28849) covalent geometry : angle 0.88647 (39099) SS BOND : bond 0.01603 ( 4) SS BOND : angle 5.01156 ( 8) hydrogen bonds : bond 0.05027 ( 1297) hydrogen bonds : angle 6.92282 ( 3645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 250 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.4176 (ttm) cc_final: 0.3852 (mtp) REVERT: C 82 MET cc_start: -0.0534 (OUTLIER) cc_final: -0.1089 (tpp) REVERT: C 129 GLU cc_start: 0.6178 (tt0) cc_final: 0.5563 (pt0) REVERT: C 144 LEU cc_start: 0.8189 (mt) cc_final: 0.7969 (mt) REVERT: C 343 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.3933 (ttt) REVERT: D 203 MET cc_start: 0.7581 (ptp) cc_final: 0.7372 (ptp) REVERT: D 246 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7178 (mp) REVERT: E 49 MET cc_start: 0.6831 (ppp) cc_final: 0.6526 (ppp) REVERT: E 122 MET cc_start: 0.2778 (mtt) cc_final: 0.2413 (mtm) REVERT: E 236 MET cc_start: 0.4089 (mmt) cc_final: 0.3852 (mmt) REVERT: E 353 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6735 (pt0) REVERT: F 46 LYS cc_start: 0.7703 (tppt) cc_final: 0.7482 (tttt) REVERT: F 49 MET cc_start: 0.4428 (ppp) cc_final: 0.3296 (mtm) REVERT: F 184 VAL cc_start: 0.7342 (OUTLIER) cc_final: 0.7001 (p) REVERT: F 330 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6839 (mmt90) REVERT: G 122 MET cc_start: 0.1150 (mtt) cc_final: -0.0278 (mtm) REVERT: G 343 MET cc_start: 0.6844 (ptt) cc_final: 0.6259 (ptt) REVERT: H 14 HIS cc_start: 0.7929 (m-70) cc_final: 0.7669 (m-70) REVERT: H 173 ASP cc_start: 0.8995 (m-30) cc_final: 0.8637 (p0) REVERT: I 254 MET cc_start: 0.6522 (tpt) cc_final: 0.5372 (tmm) REVERT: L 28 MET cc_start: 0.8692 (mmm) cc_final: 0.8056 (tpp) REVERT: L 101 LYS cc_start: 0.7684 (mttt) cc_final: 0.7364 (ptmt) REVERT: L 143 ASP cc_start: 0.9070 (t70) cc_final: 0.8797 (t0) REVERT: A 12 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.5496 (t80) REVERT: A 109 LEU cc_start: 0.5841 (mt) cc_final: 0.5386 (mt) REVERT: K 12 TYR cc_start: 0.1155 (OUTLIER) cc_final: 0.0624 (m-80) REVERT: K 13 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.6315 (t) REVERT: K 28 MET cc_start: 0.9151 (ppp) cc_final: 0.8760 (ppp) REVERT: K 33 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.7203 (m90) REVERT: K 78 LYS cc_start: 0.8369 (tmtt) cc_final: 0.7869 (mmmt) REVERT: K 80 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6838 (tm-30) REVERT: J 12 TYR cc_start: 0.5443 (m-80) cc_final: 0.5005 (m-80) REVERT: J 53 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7979 (tp) REVERT: J 75 CYS cc_start: 0.7262 (m) cc_final: 0.6962 (p) REVERT: J 109 LEU cc_start: 0.7325 (pt) cc_final: 0.6905 (pp) REVERT: J 149 TRP cc_start: 0.4002 (OUTLIER) cc_final: 0.2728 (p-90) outliers start: 154 outliers final: 86 residues processed: 375 average time/residue: 0.1698 time to fit residues: 103.3018 Evaluate side-chains 314 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 217 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 12 TYR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 311 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 341 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 384 HIS C 3 HIS C 79 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 GLN L 9 ASN ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.055469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.043814 restraints weight = 227524.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.045014 restraints weight = 156942.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.045811 restraints weight = 113236.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.046497 restraints weight = 86739.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.046820 restraints weight = 70207.636| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.8333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 28853 Z= 0.168 Angle : 0.802 14.348 39107 Z= 0.405 Chirality : 0.047 0.223 4359 Planarity : 0.006 0.060 5118 Dihedral : 6.026 47.308 3961 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 28.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.42 % Rotamer: Outliers : 4.07 % Allowed : 23.16 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.37 (0.14), residues: 3638 helix: -0.16 (0.14), residues: 1190 sheet: -0.81 (0.18), residues: 757 loop : -1.44 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 147 TYR 0.025 0.002 TYR G 338 PHE 0.035 0.002 PHE D 365 TRP 0.035 0.002 TRP I 215 HIS 0.026 0.002 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00380 (28849) covalent geometry : angle 0.79974 (39099) SS BOND : bond 0.01116 ( 4) SS BOND : angle 4.53780 ( 8) hydrogen bonds : bond 0.04263 ( 1297) hydrogen bonds : angle 6.49137 ( 3645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 248 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: B 343 MET cc_start: 0.4191 (ttm) cc_final: 0.3572 (mtp) REVERT: C 43 THR cc_start: 0.3644 (OUTLIER) cc_final: 0.3029 (p) REVERT: C 129 GLU cc_start: 0.5578 (tt0) cc_final: 0.4674 (pt0) REVERT: C 144 LEU cc_start: 0.8132 (mt) cc_final: 0.7768 (mt) REVERT: C 343 MET cc_start: 0.4605 (OUTLIER) cc_final: 0.3944 (ttt) REVERT: D 121 LEU cc_start: 0.6402 (tt) cc_final: 0.6165 (tp) REVERT: D 185 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7356 (mt) REVERT: D 246 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7127 (mp) REVERT: D 329 VAL cc_start: 0.8486 (t) cc_final: 0.8257 (p) REVERT: E 122 MET cc_start: 0.2338 (mtt) cc_final: 0.2035 (mtt) REVERT: E 236 MET cc_start: 0.3719 (mmt) cc_final: 0.3424 (mmt) REVERT: E 353 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: F 46 LYS cc_start: 0.7643 (tppt) cc_final: 0.7058 (tttt) REVERT: F 184 VAL cc_start: 0.7287 (OUTLIER) cc_final: 0.6973 (p) REVERT: F 330 ARG cc_start: 0.7285 (mtm110) cc_final: 0.6784 (mpt180) REVERT: G 122 MET cc_start: 0.1251 (mtt) cc_final: -0.0140 (mtm) REVERT: G 203 MET cc_start: 0.6593 (tpt) cc_final: 0.5942 (mtp) REVERT: G 236 MET cc_start: 0.3844 (mmm) cc_final: 0.3488 (mmm) REVERT: G 343 MET cc_start: 0.6878 (ptt) cc_final: 0.6365 (ptt) REVERT: H 14 HIS cc_start: 0.7933 (m-70) cc_final: 0.7674 (m-70) REVERT: H 173 ASP cc_start: 0.8995 (m-30) cc_final: 0.8621 (p0) REVERT: H 306 GLU cc_start: 0.7796 (pp20) cc_final: 0.7513 (pp20) REVERT: H 311 MET cc_start: 0.7640 (ttt) cc_final: 0.7310 (ttp) REVERT: I 215 TRP cc_start: 0.8433 (m-10) cc_final: 0.8204 (m-10) REVERT: I 254 MET cc_start: 0.6583 (tpt) cc_final: 0.5616 (tmm) REVERT: L 28 MET cc_start: 0.8656 (mmm) cc_final: 0.8035 (tpp) REVERT: L 101 LYS cc_start: 0.7818 (mttt) cc_final: 0.7332 (mtmt) REVERT: L 143 ASP cc_start: 0.8621 (t70) cc_final: 0.8402 (t0) REVERT: A 12 TYR cc_start: 0.5980 (OUTLIER) cc_final: 0.5489 (t80) REVERT: K 80 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6808 (tm-30) REVERT: J 12 TYR cc_start: 0.5502 (m-80) cc_final: 0.5253 (m-80) REVERT: J 75 CYS cc_start: 0.7349 (m) cc_final: 0.7130 (p) REVERT: J 109 LEU cc_start: 0.7184 (pt) cc_final: 0.6690 (pp) REVERT: J 149 TRP cc_start: 0.3880 (OUTLIER) cc_final: 0.2505 (p-90) outliers start: 122 outliers final: 76 residues processed: 344 average time/residue: 0.1732 time to fit residues: 96.6696 Evaluate side-chains 315 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 230 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 145 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 92 TRP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 298 optimal weight: 6.9990 chunk 120 optimal weight: 0.0370 chunk 15 optimal weight: 0.0470 chunk 340 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 344 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 248 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.056222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.044469 restraints weight = 223824.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.045761 restraints weight = 154375.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.046557 restraints weight = 109082.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.046904 restraints weight = 83494.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.047560 restraints weight = 70607.361| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.8404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28853 Z= 0.150 Angle : 0.788 15.621 39107 Z= 0.394 Chirality : 0.047 0.225 4359 Planarity : 0.005 0.056 5118 Dihedral : 5.657 46.589 3961 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.45 % Rotamer: Outliers : 2.87 % Allowed : 24.03 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.07 (0.14), residues: 3638 helix: 0.15 (0.15), residues: 1183 sheet: -0.58 (0.19), residues: 751 loop : -1.34 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 279 TYR 0.026 0.002 TYR G 251 PHE 0.045 0.002 PHE K 127 TRP 0.035 0.002 TRP C 159 HIS 0.019 0.001 HIS L 105 Details of bonding type rmsd covalent geometry : bond 0.00326 (28849) covalent geometry : angle 0.78447 (39099) SS BOND : bond 0.01645 ( 4) SS BOND : angle 5.49412 ( 8) hydrogen bonds : bond 0.03928 ( 1297) hydrogen bonds : angle 6.08882 ( 3645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 258 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.4450 (ttm) cc_final: 0.3967 (mtp) REVERT: C 129 GLU cc_start: 0.5409 (tt0) cc_final: 0.4840 (pt0) REVERT: C 144 LEU cc_start: 0.8111 (mt) cc_final: 0.7750 (mt) REVERT: D 121 LEU cc_start: 0.6492 (tt) cc_final: 0.6264 (tp) REVERT: D 185 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7615 (mt) REVERT: D 251 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5784 (t80) REVERT: E 122 MET cc_start: 0.2413 (mtt) cc_final: 0.2134 (mtm) REVERT: E 236 MET cc_start: 0.3879 (mmt) cc_final: 0.3520 (mmt) REVERT: E 353 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6676 (pt0) REVERT: F 46 LYS cc_start: 0.7673 (tppt) cc_final: 0.6918 (tttt) REVERT: F 245 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8252 (mmmm) REVERT: F 330 ARG cc_start: 0.7385 (mtm110) cc_final: 0.6913 (mpt180) REVERT: G 203 MET cc_start: 0.6431 (tpt) cc_final: 0.5700 (mtp) REVERT: G 236 MET cc_start: 0.3829 (mmm) cc_final: 0.3450 (mmm) REVERT: G 343 MET cc_start: 0.6805 (ptt) cc_final: 0.6335 (ptt) REVERT: H 14 HIS cc_start: 0.7880 (m-70) cc_final: 0.7610 (m-70) REVERT: H 49 MET cc_start: 0.7308 (ppp) cc_final: 0.7101 (tmm) REVERT: H 173 ASP cc_start: 0.9013 (m-30) cc_final: 0.8613 (p0) REVERT: I 215 TRP cc_start: 0.8291 (m-10) cc_final: 0.8061 (m-10) REVERT: I 254 MET cc_start: 0.6519 (tpt) cc_final: 0.5617 (tmm) REVERT: L 28 MET cc_start: 0.8721 (mmm) cc_final: 0.7987 (tpp) REVERT: L 143 ASP cc_start: 0.8592 (t70) cc_final: 0.8388 (t0) REVERT: A 12 TYR cc_start: 0.5630 (OUTLIER) cc_final: 0.5291 (t80) REVERT: K 33 HIS cc_start: 0.7544 (t-90) cc_final: 0.7099 (m-70) REVERT: K 80 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6872 (tm-30) REVERT: J 75 CYS cc_start: 0.7305 (m) cc_final: 0.7012 (p) REVERT: J 109 LEU cc_start: 0.7049 (pt) cc_final: 0.6823 (pp) REVERT: J 149 TRP cc_start: 0.3873 (OUTLIER) cc_final: 0.2413 (p-90) outliers start: 86 outliers final: 62 residues processed: 326 average time/residue: 0.1739 time to fit residues: 92.8692 Evaluate side-chains 295 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 228 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 285 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 334 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.055021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.043632 restraints weight = 231500.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.044816 restraints weight = 158357.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.045576 restraints weight = 114036.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.046191 restraints weight = 87136.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.046513 restraints weight = 72128.150| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.9131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28853 Z= 0.180 Angle : 0.803 13.812 39107 Z= 0.406 Chirality : 0.048 0.274 4359 Planarity : 0.006 0.086 5118 Dihedral : 5.820 47.049 3961 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.44 % Allowed : 23.66 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.18 (0.14), residues: 3638 helix: 0.06 (0.15), residues: 1182 sheet: -0.75 (0.19), residues: 752 loop : -1.34 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG L 74 TYR 0.035 0.002 TYR L 57 PHE 0.033 0.002 PHE D 365 TRP 0.035 0.002 TRP E 367 HIS 0.018 0.002 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00402 (28849) covalent geometry : angle 0.80020 (39099) SS BOND : bond 0.00727 ( 4) SS BOND : angle 4.91616 ( 8) hydrogen bonds : bond 0.04135 ( 1297) hydrogen bonds : angle 6.27903 ( 3645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 244 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 TYR cc_start: 0.6951 (t80) cc_final: 0.6542 (m-80) REVERT: B 343 MET cc_start: 0.4715 (ttm) cc_final: 0.4392 (mtp) REVERT: C 77 TYR cc_start: 0.6365 (m-10) cc_final: 0.6065 (m-10) REVERT: C 129 GLU cc_start: 0.6071 (tt0) cc_final: 0.5410 (pt0) REVERT: C 144 LEU cc_start: 0.8284 (mt) cc_final: 0.7913 (mt) REVERT: C 343 MET cc_start: 0.5574 (ttm) cc_final: 0.5092 (ttm) REVERT: D 121 LEU cc_start: 0.7333 (tt) cc_final: 0.7054 (tp) REVERT: D 134 MET cc_start: 0.0837 (mmm) cc_final: 0.0374 (mmm) REVERT: D 185 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7529 (mt) REVERT: D 246 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7342 (mp) REVERT: D 251 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5912 (t80) REVERT: E 122 MET cc_start: 0.2784 (mtt) cc_final: 0.2441 (mtm) REVERT: E 191 GLU cc_start: 0.8374 (tp30) cc_final: 0.8021 (mp0) REVERT: E 236 MET cc_start: 0.3865 (mmt) cc_final: 0.3384 (mmt) REVERT: E 353 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: F 184 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7185 (p) REVERT: F 245 LYS cc_start: 0.8547 (mmtp) cc_final: 0.8270 (mmmm) REVERT: F 330 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7239 (mmt90) REVERT: G 65 GLU cc_start: 0.3526 (OUTLIER) cc_final: 0.2348 (mt-10) REVERT: G 122 MET cc_start: 0.2281 (mtt) cc_final: 0.1105 (mtm) REVERT: G 203 MET cc_start: 0.7140 (tpt) cc_final: 0.6467 (mtt) REVERT: G 236 MET cc_start: 0.3822 (mmm) cc_final: 0.3599 (mmm) REVERT: G 343 MET cc_start: 0.7103 (ptt) cc_final: 0.6573 (ptt) REVERT: H 14 HIS cc_start: 0.8020 (m-70) cc_final: 0.7725 (m-70) REVERT: H 49 MET cc_start: 0.7593 (ppp) cc_final: 0.6485 (tmm) REVERT: H 113 GLU cc_start: 0.7903 (tp30) cc_final: 0.7399 (pp20) REVERT: H 173 ASP cc_start: 0.8994 (m-30) cc_final: 0.8593 (p0) REVERT: H 311 MET cc_start: 0.7460 (ttt) cc_final: 0.7131 (ttp) REVERT: I 215 TRP cc_start: 0.8370 (m-10) cc_final: 0.8114 (m-10) REVERT: I 254 MET cc_start: 0.6668 (tpt) cc_final: 0.5809 (tmm) REVERT: I 311 MET cc_start: 0.4617 (mmt) cc_final: 0.4250 (mmt) REVERT: L 28 MET cc_start: 0.8699 (mmm) cc_final: 0.8007 (tpp) REVERT: L 101 LYS cc_start: 0.6552 (mtmt) cc_final: 0.6158 (ttpt) REVERT: L 143 ASP cc_start: 0.8680 (t70) cc_final: 0.8402 (t0) REVERT: A 12 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5587 (t80) REVERT: K 33 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6689 (m90) REVERT: K 80 GLN cc_start: 0.7303 (tm-30) cc_final: 0.6882 (tm-30) REVERT: J 75 CYS cc_start: 0.7845 (m) cc_final: 0.7417 (p) REVERT: J 149 TRP cc_start: 0.4431 (OUTLIER) cc_final: 0.2961 (p-90) outliers start: 103 outliers final: 74 residues processed: 321 average time/residue: 0.1714 time to fit residues: 89.5075 Evaluate side-chains 315 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 232 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 347 optimal weight: 0.0570 chunk 312 optimal weight: 20.0000 chunk 302 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 overall best weight: 3.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN H 98 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS K 150 GLN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.054600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.043399 restraints weight = 236863.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.044396 restraints weight = 170263.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.045060 restraints weight = 128984.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.045387 restraints weight = 101518.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.045638 restraints weight = 87186.148| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 1.0066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 28853 Z= 0.190 Angle : 0.830 13.715 39107 Z= 0.417 Chirality : 0.048 0.288 4359 Planarity : 0.006 0.060 5118 Dihedral : 5.930 41.781 3961 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 29.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 3.10 % Allowed : 24.30 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.26 (0.14), residues: 3638 helix: 0.07 (0.15), residues: 1173 sheet: -0.89 (0.18), residues: 762 loop : -1.39 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 279 TYR 0.021 0.002 TYR C 280 PHE 0.043 0.002 PHE D 365 TRP 0.050 0.002 TRP E 367 HIS 0.014 0.002 HIS L 105 Details of bonding type rmsd covalent geometry : bond 0.00412 (28849) covalent geometry : angle 0.82726 (39099) SS BOND : bond 0.00731 ( 4) SS BOND : angle 4.34980 ( 8) hydrogen bonds : bond 0.04136 ( 1297) hydrogen bonds : angle 6.33165 ( 3645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 245 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 TYR cc_start: 0.7529 (t80) cc_final: 0.7016 (m-80) REVERT: B 343 MET cc_start: 0.5214 (ttm) cc_final: 0.4821 (mtp) REVERT: C 49 MET cc_start: 0.6045 (mmm) cc_final: 0.5535 (mmm) REVERT: C 144 LEU cc_start: 0.8490 (mt) cc_final: 0.8097 (mt) REVERT: C 343 MET cc_start: 0.6866 (ttm) cc_final: 0.6424 (ttm) REVERT: D 8 GLU cc_start: 0.6564 (tm-30) cc_final: 0.6166 (tp30) REVERT: D 121 LEU cc_start: 0.7722 (tt) cc_final: 0.7454 (tp) REVERT: D 134 MET cc_start: 0.1572 (mmm) cc_final: 0.1087 (mmm) REVERT: D 185 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7757 (mt) REVERT: D 246 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7668 (mp) REVERT: D 251 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.5876 (t80) REVERT: E 191 GLU cc_start: 0.8657 (tp30) cc_final: 0.8272 (mp0) REVERT: E 236 MET cc_start: 0.4332 (mmt) cc_final: 0.4036 (mmt) REVERT: E 353 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7168 (pt0) REVERT: F 44 TYR cc_start: 0.7420 (t80) cc_final: 0.6834 (t80) REVERT: F 184 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7235 (p) REVERT: F 245 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8251 (mmmt) REVERT: F 330 ARG cc_start: 0.8191 (mtm110) cc_final: 0.7521 (mmt90) REVERT: G 46 LYS cc_start: 0.8557 (tppt) cc_final: 0.7442 (tttm) REVERT: G 65 GLU cc_start: 0.3386 (OUTLIER) cc_final: 0.2194 (mt-10) REVERT: G 122 MET cc_start: 0.2682 (mtt) cc_final: 0.1649 (mtm) REVERT: G 203 MET cc_start: 0.8030 (tpt) cc_final: 0.7430 (mtt) REVERT: G 236 MET cc_start: 0.4158 (mmm) cc_final: 0.3723 (mmm) REVERT: G 343 MET cc_start: 0.7271 (ptt) cc_final: 0.6638 (ptt) REVERT: H 14 HIS cc_start: 0.8077 (m-70) cc_final: 0.7819 (m-70) REVERT: H 173 ASP cc_start: 0.9095 (m-30) cc_final: 0.8755 (p0) REVERT: H 311 MET cc_start: 0.7342 (ttt) cc_final: 0.7036 (ttp) REVERT: I 134 MET cc_start: 0.2755 (mmm) cc_final: 0.2530 (mmm) REVERT: I 215 TRP cc_start: 0.8667 (m-10) cc_final: 0.8439 (m-10) REVERT: I 254 MET cc_start: 0.6723 (tpt) cc_final: 0.6093 (tmm) REVERT: I 311 MET cc_start: 0.4902 (mmt) cc_final: 0.4441 (mmt) REVERT: L 28 MET cc_start: 0.8752 (mmm) cc_final: 0.8144 (tpp) REVERT: L 101 LYS cc_start: 0.6818 (mtmt) cc_final: 0.6614 (ttpt) REVERT: L 143 ASP cc_start: 0.8837 (t70) cc_final: 0.8536 (t0) REVERT: A 12 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.5528 (t80) REVERT: K 33 HIS cc_start: 0.7490 (t70) cc_final: 0.6969 (m90) REVERT: K 80 GLN cc_start: 0.7433 (tm-30) cc_final: 0.7045 (tm-30) REVERT: J 149 TRP cc_start: 0.4805 (OUTLIER) cc_final: 0.3203 (p-90) outliers start: 93 outliers final: 68 residues processed: 319 average time/residue: 0.1755 time to fit residues: 91.8567 Evaluate side-chains 305 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 229 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 90 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 360 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 197 optimal weight: 1.9990 chunk 205 optimal weight: 0.0170 chunk 302 optimal weight: 0.2980 chunk 268 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.055673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.044160 restraints weight = 226457.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.045292 restraints weight = 155556.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.046097 restraints weight = 112292.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.046453 restraints weight = 86309.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.047171 restraints weight = 73103.396| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 1.0143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28853 Z= 0.147 Angle : 0.824 20.055 39107 Z= 0.405 Chirality : 0.048 0.323 4359 Planarity : 0.005 0.089 5118 Dihedral : 5.573 35.235 3960 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.14 % Allowed : 25.53 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.09 (0.14), residues: 3638 helix: 0.17 (0.15), residues: 1183 sheet: -0.68 (0.19), residues: 738 loop : -1.34 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 362 TYR 0.022 0.002 TYR C 280 PHE 0.032 0.002 PHE F 360 TRP 0.038 0.002 TRP E 367 HIS 0.013 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00330 (28849) covalent geometry : angle 0.82184 (39099) SS BOND : bond 0.00847 ( 4) SS BOND : angle 3.88484 ( 8) hydrogen bonds : bond 0.03862 ( 1297) hydrogen bonds : angle 6.01317 ( 3645) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 TYR cc_start: 0.6970 (t80) cc_final: 0.6549 (m-80) REVERT: B 343 MET cc_start: 0.4899 (ttm) cc_final: 0.4562 (mtp) REVERT: C 129 GLU cc_start: 0.5935 (tt0) cc_final: 0.5715 (pt0) REVERT: C 144 LEU cc_start: 0.8450 (mt) cc_final: 0.8041 (mt) REVERT: C 343 MET cc_start: 0.6715 (ttm) cc_final: 0.6353 (ttm) REVERT: D 66 GLU cc_start: 0.4239 (mp0) cc_final: 0.3902 (mp0) REVERT: D 121 LEU cc_start: 0.7564 (tt) cc_final: 0.7242 (tp) REVERT: D 122 MET cc_start: 0.6483 (mtt) cc_final: 0.5884 (mtt) REVERT: D 134 MET cc_start: 0.1375 (mmm) cc_final: 0.1033 (mmm) REVERT: D 185 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7924 (mt) REVERT: D 251 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.5500 (t80) REVERT: D 311 MET cc_start: 0.6143 (tmm) cc_final: 0.5328 (tpt) REVERT: E 122 MET cc_start: 0.2868 (mtt) cc_final: 0.2662 (mtt) REVERT: E 191 GLU cc_start: 0.8316 (tp30) cc_final: 0.8025 (mp0) REVERT: E 236 MET cc_start: 0.4212 (mmt) cc_final: 0.3924 (mmt) REVERT: F 184 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7300 (p) REVERT: F 236 MET cc_start: 0.7582 (mmt) cc_final: 0.7195 (mmt) REVERT: F 245 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8319 (mmmt) REVERT: F 290 LEU cc_start: 0.5726 (mp) cc_final: 0.4629 (mt) REVERT: F 295 GLU cc_start: 0.7152 (tt0) cc_final: 0.6316 (tp30) REVERT: F 330 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7486 (mmt90) REVERT: G 122 MET cc_start: 0.2671 (mtt) cc_final: 0.1550 (mtm) REVERT: G 236 MET cc_start: 0.4497 (mmm) cc_final: 0.3892 (mmm) REVERT: G 296 ILE cc_start: 0.7778 (mm) cc_final: 0.7208 (tp) REVERT: G 343 MET cc_start: 0.7334 (ptt) cc_final: 0.6668 (ptt) REVERT: H 14 HIS cc_start: 0.7996 (m-70) cc_final: 0.7714 (m-70) REVERT: H 49 MET cc_start: 0.7854 (ppp) cc_final: 0.7535 (ttp) REVERT: H 82 MET cc_start: -0.0990 (mmt) cc_final: -0.1196 (tpt) REVERT: H 311 MET cc_start: 0.7328 (ttt) cc_final: 0.7097 (ttp) REVERT: I 134 MET cc_start: 0.2658 (mmm) cc_final: 0.2434 (mmm) REVERT: I 215 TRP cc_start: 0.8414 (m-10) cc_final: 0.8152 (m-10) REVERT: I 254 MET cc_start: 0.6582 (tpt) cc_final: 0.5996 (tmm) REVERT: L 28 MET cc_start: 0.8653 (mmm) cc_final: 0.8020 (tpp) REVERT: L 143 ASP cc_start: 0.8721 (t70) cc_final: 0.8438 (t0) REVERT: K 33 HIS cc_start: 0.7235 (t70) cc_final: 0.6794 (m90) REVERT: K 80 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6978 (tm-30) REVERT: J 149 TRP cc_start: 0.4521 (OUTLIER) cc_final: 0.2780 (p-90) outliers start: 64 outliers final: 53 residues processed: 292 average time/residue: 0.1795 time to fit residues: 85.4878 Evaluate side-chains 278 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 262 PHE Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 308 optimal weight: 0.0570 chunk 212 optimal weight: 0.0020 chunk 352 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 348 optimal weight: 0.0770 chunk 314 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.055403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.044108 restraints weight = 230247.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.045276 restraints weight = 159269.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.046017 restraints weight = 113415.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.046558 restraints weight = 87607.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.047124 restraints weight = 73273.815| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 1.0391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28853 Z= 0.143 Angle : 0.801 15.108 39107 Z= 0.395 Chirality : 0.047 0.343 4359 Planarity : 0.005 0.095 5118 Dihedral : 5.490 33.372 3960 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.17 % Allowed : 25.53 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.02 (0.14), residues: 3638 helix: 0.26 (0.15), residues: 1181 sheet: -0.65 (0.19), residues: 733 loop : -1.31 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 147 TYR 0.024 0.002 TYR A 100 PHE 0.034 0.002 PHE D 365 TRP 0.039 0.002 TRP C 159 HIS 0.012 0.001 HIS L 105 Details of bonding type rmsd covalent geometry : bond 0.00324 (28849) covalent geometry : angle 0.79921 (39099) SS BOND : bond 0.00797 ( 4) SS BOND : angle 3.72798 ( 8) hydrogen bonds : bond 0.03815 ( 1297) hydrogen bonds : angle 5.96256 ( 3645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5554.14 seconds wall clock time: 97 minutes 17.72 seconds (5837.72 seconds total)