Starting phenix.real_space_refine on Mon Aug 25 22:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frs_29406/08_2025/8frs_29406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frs_29406/08_2025/8frs_29406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8frs_29406/08_2025/8frs_29406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frs_29406/08_2025/8frs_29406.map" model { file = "/net/cci-nas-00/data/ceres_data/8frs_29406/08_2025/8frs_29406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frs_29406/08_2025/8frs_29406.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 78 5.16 5 C 19970 2.51 5 N 5370 2.21 5 O 6079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31497 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "C" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "D" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "E" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "F" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "f" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1523 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "g" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1523 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "h" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1523 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "H" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "G" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "I" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "J" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain: "K" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2448 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Time building chain proxies: 7.81, per 1000 atoms: 0.25 Number of scatterers: 31497 At special positions: 0 Unit cell: (281.12, 247.52, 137.76, 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 78 16.00 O 6079 8.00 N 5370 7.00 C 19970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7462 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 57 sheets defined 24.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.814A pdb=" N ILE B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 197 Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.692A pdb=" N ILE B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.815A pdb=" N GLU B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.901A pdb=" N LEU B 302 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.976A pdb=" N ILE A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.535A pdb=" N GLY A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.509A pdb=" N ALA A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.729A pdb=" N GLU A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 removed outlier: 5.200A pdb=" N ASP A 271 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 272 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 273 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 274 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 275 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.538A pdb=" N LEU A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.546A pdb=" N ILE C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.764A pdb=" N GLY C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 174 through 197 removed outlier: 3.546A pdb=" N ALA C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 250 removed outlier: 3.595A pdb=" N ASP C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.189A pdb=" N GLU C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.572A pdb=" N SER C 274 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.765A pdb=" N ILE D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 removed outlier: 3.673A pdb=" N GLY D 166 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 174 through 197 removed outlier: 3.528A pdb=" N ALA D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 250 removed outlier: 3.556A pdb=" N ILE D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 removed outlier: 4.096A pdb=" N GLU D 259 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.577A pdb=" N TRP D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 removed outlier: 3.521A pdb=" N SER D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.702A pdb=" N ILE E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 169 Processing helix chain 'E' and resid 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 174 through 197 removed outlier: 3.532A pdb=" N ALA E 184 " --> pdb=" O ARG E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 250 Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.645A pdb=" N GLU E 259 " --> pdb=" O PRO E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 275 removed outlier: 3.567A pdb=" N VAL E 270 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP E 271 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 273 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER E 274 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 291 Processing helix chain 'E' and resid 299 through 303 removed outlier: 3.741A pdb=" N LEU E 302 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.716A pdb=" N ILE F 103 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 169 removed outlier: 3.579A pdb=" N GLY F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 174 through 197 Processing helix chain 'F' and resid 231 through 250 removed outlier: 3.675A pdb=" N ILE F 239 " --> pdb=" O ILE F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 4.040A pdb=" N GLU F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.602A pdb=" N LEU F 273 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 274 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.549A pdb=" N TRP F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 324 through 329 Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'f' and resid 33 through 37 Processing helix chain 'f' and resid 90 through 94 removed outlier: 3.588A pdb=" N TYR f 94 " --> pdb=" O PRO f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 37 Processing helix chain 'g' and resid 90 through 94 Processing helix chain 'g' and resid 153 through 157 Processing helix chain 'h' and resid 33 through 37 Processing helix chain 'h' and resid 90 through 94 Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 162 through 171 removed outlier: 3.677A pdb=" N ALA H 170 " --> pdb=" O GLY H 166 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 197 Processing helix chain 'H' and resid 231 through 250 Processing helix chain 'H' and resid 269 through 275 Processing helix chain 'H' and resid 282 through 291 Processing helix chain 'H' and resid 299 through 303 Processing helix chain 'H' and resid 372 through 374 No H-bonds generated for 'chain 'H' and resid 372 through 374' Processing helix chain 'G' and resid 99 through 104 Processing helix chain 'G' and resid 162 through 171 removed outlier: 3.519A pdb=" N ALA G 170 " --> pdb=" O GLY G 166 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 197 Processing helix chain 'G' and resid 231 through 250 removed outlier: 3.673A pdb=" N ILE G 239 " --> pdb=" O ILE G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 275 Processing helix chain 'G' and resid 282 through 291 Processing helix chain 'G' and resid 299 through 303 Processing helix chain 'G' and resid 372 through 374 No H-bonds generated for 'chain 'G' and resid 372 through 374' Processing helix chain 'I' and resid 99 through 104 Processing helix chain 'I' and resid 162 through 171 removed outlier: 3.639A pdb=" N ALA I 170 " --> pdb=" O GLY I 166 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 197 Processing helix chain 'I' and resid 231 through 250 removed outlier: 3.645A pdb=" N ILE I 239 " --> pdb=" O ILE I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 275 Processing helix chain 'I' and resid 282 through 291 Processing helix chain 'I' and resid 299 through 303 Processing helix chain 'I' and resid 372 through 374 No H-bonds generated for 'chain 'I' and resid 372 through 374' Processing helix chain 'J' and resid 99 through 104 Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.593A pdb=" N ALA J 170 " --> pdb=" O GLY J 166 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 197 Processing helix chain 'J' and resid 231 through 250 removed outlier: 3.659A pdb=" N ILE J 239 " --> pdb=" O ILE J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 275 Processing helix chain 'J' and resid 282 through 291 Processing helix chain 'J' and resid 299 through 303 Processing helix chain 'J' and resid 372 through 374 No H-bonds generated for 'chain 'J' and resid 372 through 374' Processing helix chain 'K' and resid 99 through 105 removed outlier: 3.772A pdb=" N ILE K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 169 Processing helix chain 'K' and resid 170 through 172 No H-bonds generated for 'chain 'K' and resid 170 through 172' Processing helix chain 'K' and resid 174 through 197 Processing helix chain 'K' and resid 231 through 250 removed outlier: 3.512A pdb=" N ASP K 238 " --> pdb=" O GLY K 234 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE K 239 " --> pdb=" O ILE K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 275 Processing helix chain 'K' and resid 282 through 291 Processing helix chain 'K' and resid 299 through 303 Processing helix chain 'K' and resid 372 through 374 No H-bonds generated for 'chain 'K' and resid 372 through 374' Processing sheet with id=AA1, first strand: chain 'B' and resid 84 through 86 removed outlier: 3.552A pdb=" N ILE F 117 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN F 145 " --> pdb=" O ILE F 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 107 through 108 removed outlier: 5.875A pdb=" N ASP B 107 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER B 343 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N GLN B 339 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N CYS B 370 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N VAL B 341 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N ALA B 368 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N SER B 343 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA B 366 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE B 345 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLY B 364 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR B 347 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 362 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 349 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 150 removed outlier: 13.047A pdb=" N GLU B 116 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 13.729A pdb=" N GLY A 89 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N VAL B 118 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N VAL A 91 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY B 120 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.503A pdb=" N VAL A 160 " --> pdb=" O TYR A 357 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 357 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 349 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 362 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR A 347 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY A 364 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE A 345 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA7, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.437A pdb=" N GLU A 116 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU C 87 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 118 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY C 89 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY A 120 " --> pdb=" O GLY C 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.526A pdb=" N VAL C 160 " --> pdb=" O TYR C 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 357 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY C 349 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 362 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR C 347 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY C 364 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE C 345 " --> pdb=" O GLY C 364 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ALA C 366 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 11.180A pdb=" N SER C 343 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA C 368 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N VAL C 341 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N CYS C 370 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N GLN C 339 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP C 107 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER C 343 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB2, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.654A pdb=" N GLY A 367 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 150 removed outlier: 3.669A pdb=" N ILE C 117 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU C 116 " --> pdb=" O THR D 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 124 through 126 removed outlier: 3.524A pdb=" N SER C 141 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.513A pdb=" N VAL D 160 " --> pdb=" O TYR D 357 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 357 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY D 349 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER D 362 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR D 347 " --> pdb=" O SER D 362 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLY D 364 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE D 345 " --> pdb=" O GLY D 364 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA D 366 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N SER D 343 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N ALA D 368 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N VAL D 341 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N CYS D 370 " --> pdb=" O GLN D 339 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N GLN D 339 " --> pdb=" O CYS D 370 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP D 107 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER D 343 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AB7, first strand: chain 'D' and resid 145 through 150 removed outlier: 6.611A pdb=" N GLU D 116 " --> pdb=" O THR E 85 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU E 87 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 118 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY E 89 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY D 120 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AB9, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.570A pdb=" N VAL E 160 " --> pdb=" O TYR E 357 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR E 357 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 11.826A pdb=" N SER E 356 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL E 350 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 11.480A pdb=" N VAL E 358 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LEU E 348 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP E 360 " --> pdb=" O ILE E 346 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE E 346 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER E 362 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS E 344 " --> pdb=" O SER E 362 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY E 364 " --> pdb=" O GLN E 342 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 342 " --> pdb=" O GLY E 364 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU E 340 " --> pdb=" O ALA E 366 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA E 368 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER E 338 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP E 107 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER E 343 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 295 through 296 Processing sheet with id=AC2, first strand: chain 'E' and resid 145 through 150 removed outlier: 6.551A pdb=" N GLU E 116 " --> pdb=" O THR F 85 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU F 87 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL E 118 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLY F 89 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY E 120 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=AC4, first strand: chain 'E' and resid 129 through 130 removed outlier: 11.473A pdb=" N SER F 356 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N VAL F 350 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N VAL F 358 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N LEU F 348 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP F 360 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE F 346 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER F 362 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS F 344 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY F 364 " --> pdb=" O GLN F 342 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU F 340 " --> pdb=" O ALA F 366 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA F 368 " --> pdb=" O SER F 338 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER F 338 " --> pdb=" O ALA F 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 137 through 138 removed outlier: 4.077A pdb=" N ILE E 137 " --> pdb=" O ASP h 21 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY h 124 " --> pdb=" O ILE h 19 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 295 through 296 Processing sheet with id=AC7, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AC8, first strand: chain 'F' and resid 295 through 296 Processing sheet with id=AC9, first strand: chain 'f' and resid 25 through 31 removed outlier: 10.951A pdb=" N SER f 75 " --> pdb=" O ALA f 26 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL f 77 " --> pdb=" O PRO f 28 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG f 30 " --> pdb=" O VAL f 77 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU f 76 " --> pdb=" O ALA f 56 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE f 53 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 12.420A pdb=" N PHE f 85 " --> pdb=" O MET f 121 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET f 121 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLU f 115 " --> pdb=" O ILE f 31 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE f 31 " --> pdb=" O GLU f 115 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU f 117 " --> pdb=" O GLY f 29 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY f 29 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE f 119 " --> pdb=" O ARG f 27 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG f 27 " --> pdb=" O PHE f 119 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 179 through 180 removed outlier: 4.278A pdb=" N LEU f 166 " --> pdb=" O GLU f 128 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY f 168 " --> pdb=" O PHE f 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 137 through 138 Processing sheet with id=AD3, first strand: chain 'g' and resid 205 through 208 removed outlier: 7.628A pdb=" N MET g 121 " --> pdb=" O PHE g 85 " (cutoff:3.500A) removed outlier: 12.440A pdb=" N PHE g 85 " --> pdb=" O MET g 121 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE g 53 " --> pdb=" O PHE g 85 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU g 76 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N SER g 75 " --> pdb=" O ALA g 26 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL g 77 " --> pdb=" O PRO g 28 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG g 30 " --> pdb=" O VAL g 77 " (cutoff:3.500A) removed outlier: 10.786A pdb=" N ASP g 17 " --> pdb=" O GLU g 128 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N GLU g 128 " --> pdb=" O ASP g 17 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE g 19 " --> pdb=" O VAL g 126 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL g 126 " --> pdb=" O ILE g 19 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP g 21 " --> pdb=" O GLY g 124 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY g 124 " --> pdb=" O ASP g 21 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA g 122 " --> pdb=" O PRO g 23 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG g 25 " --> pdb=" O ASP g 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'g' and resid 137 through 138 Processing sheet with id=AD5, first strand: chain 'g' and resid 166 through 169 Processing sheet with id=AD6, first strand: chain 'h' and resid 25 through 31 removed outlier: 11.271A pdb=" N SER h 75 " --> pdb=" O ALA h 26 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL h 77 " --> pdb=" O PRO h 28 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG h 30 " --> pdb=" O VAL h 77 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU h 76 " --> pdb=" O ALA h 56 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE h 53 " --> pdb=" O PHE h 85 " (cutoff:3.500A) removed outlier: 12.487A pdb=" N PHE h 85 " --> pdb=" O MET h 121 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N MET h 121 " --> pdb=" O PHE h 85 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU h 115 " --> pdb=" O ILE h 31 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE h 31 " --> pdb=" O GLU h 115 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU h 117 " --> pdb=" O GLY h 29 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY h 29 " --> pdb=" O GLU h 117 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE h 119 " --> pdb=" O ARG h 27 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG h 27 " --> pdb=" O PHE h 119 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'h' and resid 179 through 180 removed outlier: 4.665A pdb=" N LEU h 166 " --> pdb=" O GLU h 128 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY h 168 " --> pdb=" O PHE h 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'h' and resid 137 through 138 Processing sheet with id=AD9, first strand: chain 'H' and resid 84 through 91 removed outlier: 3.529A pdb=" N THR H 85 " --> pdb=" O GLU G 116 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY G 120 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY H 89 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 145 through 150 removed outlier: 13.229A pdb=" N GLU H 116 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 13.179A pdb=" N GLY K 89 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N VAL H 118 " --> pdb=" O GLY K 89 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N VAL K 91 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY H 120 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 124 through 125 Processing sheet with id=AE3, first strand: chain 'H' and resid 152 through 161 removed outlier: 11.752A pdb=" N SER H 356 " --> pdb=" O VAL H 350 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N VAL H 350 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N VAL H 358 " --> pdb=" O LEU H 348 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N LEU H 348 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP H 360 " --> pdb=" O ILE H 346 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE H 346 " --> pdb=" O ASP H 360 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER H 362 " --> pdb=" O LYS H 344 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS H 344 " --> pdb=" O SER H 362 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY H 364 " --> pdb=" O GLN H 342 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU H 340 " --> pdb=" O ALA H 366 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA H 368 " --> pdb=" O SER H 338 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER H 338 " --> pdb=" O ALA H 368 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 295 through 296 Processing sheet with id=AE5, first strand: chain 'G' and resid 84 through 86 removed outlier: 6.930A pdb=" N THR G 85 " --> pdb=" O VAL I 118 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N GLY I 120 " --> pdb=" O THR G 85 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 124 through 125 Processing sheet with id=AE7, first strand: chain 'G' and resid 152 through 161 removed outlier: 11.678A pdb=" N SER G 356 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N VAL G 350 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 11.684A pdb=" N VAL G 358 " --> pdb=" O LEU G 348 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU G 348 " --> pdb=" O VAL G 358 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASP G 360 " --> pdb=" O ILE G 346 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE G 346 " --> pdb=" O ASP G 360 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER G 362 " --> pdb=" O LYS G 344 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS G 344 " --> pdb=" O SER G 362 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY G 364 " --> pdb=" O GLN G 342 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU G 340 " --> pdb=" O ALA G 366 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA G 368 " --> pdb=" O SER G 338 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER G 338 " --> pdb=" O ALA G 368 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 295 through 296 removed outlier: 3.554A pdb=" N LEU G 316 " --> pdb=" O TYR G 379 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 84 through 91 removed outlier: 3.528A pdb=" N THR I 85 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY J 120 " --> pdb=" O LEU I 87 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY I 89 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 124 through 125 Processing sheet with id=AF2, first strand: chain 'I' and resid 152 through 161 removed outlier: 3.516A pdb=" N ASP I 360 " --> pdb=" O GLY I 349 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY I 349 " --> pdb=" O ASP I 360 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER I 362 " --> pdb=" O THR I 347 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR I 347 " --> pdb=" O SER I 362 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLY I 364 " --> pdb=" O PHE I 345 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE I 345 " --> pdb=" O GLY I 364 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 295 through 296 Processing sheet with id=AF4, first strand: chain 'I' and resid 337 through 339 Processing sheet with id=AF5, first strand: chain 'J' and resid 84 through 91 removed outlier: 6.244A pdb=" N GLY K 120 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY J 89 " --> pdb=" O GLY K 120 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 124 through 125 Processing sheet with id=AF7, first strand: chain 'J' and resid 152 through 161 removed outlier: 3.574A pdb=" N ASP J 360 " --> pdb=" O GLY J 349 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY J 349 " --> pdb=" O ASP J 360 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER J 362 " --> pdb=" O THR J 347 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N THR J 347 " --> pdb=" O SER J 362 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLY J 364 " --> pdb=" O PHE J 345 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE J 345 " --> pdb=" O GLY J 364 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 295 through 296 Processing sheet with id=AF9, first strand: chain 'J' and resid 337 through 340 removed outlier: 3.866A pdb=" N GLY J 367 " --> pdb=" O LEU J 340 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AG2, first strand: chain 'K' and resid 152 through 161 removed outlier: 11.652A pdb=" N SER K 356 " --> pdb=" O VAL K 350 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N VAL K 350 " --> pdb=" O SER K 356 " (cutoff:3.500A) removed outlier: 11.666A pdb=" N VAL K 358 " --> pdb=" O LEU K 348 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LEU K 348 " --> pdb=" O VAL K 358 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP K 360 " --> pdb=" O ILE K 346 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE K 346 " --> pdb=" O ASP K 360 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER K 362 " --> pdb=" O LYS K 344 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS K 344 " --> pdb=" O SER K 362 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY K 364 " --> pdb=" O GLN K 342 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU K 340 " --> pdb=" O ALA K 366 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA K 368 " --> pdb=" O SER K 338 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER K 338 " --> pdb=" O ALA K 368 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 295 through 296 976 hydrogen bonds defined for protein. 2490 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: 6.35 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10513 1.34 - 1.46: 6865 1.46 - 1.58: 14656 1.58 - 1.70: 0 1.70 - 1.81: 145 Bond restraints: 32179 Sorted by residual: bond pdb=" C ASN g 38 " pdb=" N PRO g 39 " ideal model delta sigma weight residual 1.334 1.353 -0.020 8.40e-03 1.42e+04 5.60e+00 bond pdb=" C ASN h 38 " pdb=" N PRO h 39 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.57e+00 bond pdb=" C ALA K 125 " pdb=" N GLY K 126 " ideal model delta sigma weight residual 1.319 1.335 -0.016 1.34e-02 5.57e+03 1.40e+00 bond pdb=" C ALA J 125 " pdb=" N GLY J 126 " ideal model delta sigma weight residual 1.319 1.334 -0.015 1.34e-02 5.57e+03 1.32e+00 bond pdb=" C ALA I 125 " pdb=" N GLY I 126 " ideal model delta sigma weight residual 1.319 1.334 -0.015 1.34e-02 5.57e+03 1.31e+00 ... (remaining 32174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 42984 1.76 - 3.51: 771 3.51 - 5.27: 59 5.27 - 7.03: 11 7.03 - 8.79: 4 Bond angle restraints: 43829 Sorted by residual: angle pdb=" C MET G 94 " pdb=" N THR G 95 " pdb=" CA THR G 95 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C MET K 94 " pdb=" N THR K 95 " pdb=" CA THR K 95 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C MET A 94 " pdb=" N THR A 95 " pdb=" CA THR A 95 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N VAL J 129 " pdb=" CA VAL J 129 " pdb=" C VAL J 129 " ideal model delta sigma weight residual 113.20 110.02 3.18 9.60e-01 1.09e+00 1.09e+01 angle pdb=" C MET E 94 " pdb=" N THR E 95 " pdb=" CA THR E 95 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 ... (remaining 43824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17419 17.95 - 35.91: 1309 35.91 - 53.86: 239 53.86 - 71.82: 69 71.82 - 89.77: 61 Dihedral angle restraints: 19097 sinusoidal: 7420 harmonic: 11677 Sorted by residual: dihedral pdb=" CA VAL J 93 " pdb=" C VAL J 93 " pdb=" N MET J 94 " pdb=" CA MET J 94 " ideal model delta harmonic sigma weight residual 180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LYS J 308 " pdb=" C LYS J 308 " pdb=" N ASN J 309 " pdb=" CA ASN J 309 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LYS K 308 " pdb=" C LYS K 308 " pdb=" N ASN K 309 " pdb=" CA ASN K 309 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 19094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3259 0.033 - 0.066: 1074 0.066 - 0.098: 298 0.098 - 0.131: 281 0.131 - 0.164: 26 Chirality restraints: 4938 Sorted by residual: chirality pdb=" CA ILE A 121 " pdb=" N ILE A 121 " pdb=" C ILE A 121 " pdb=" CB ILE A 121 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA ILE G 117 " pdb=" N ILE G 117 " pdb=" C ILE G 117 " pdb=" CB ILE G 117 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE K 117 " pdb=" N ILE K 117 " pdb=" C ILE K 117 " pdb=" CB ILE K 117 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 4935 not shown) Planarity restraints: 5745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL h 148 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO h 149 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO h 149 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO h 149 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL g 148 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO g 149 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO g 149 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO g 149 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 216 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO F 217 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 217 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 217 " 0.024 5.00e-02 4.00e+02 ... (remaining 5742 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3078 2.75 - 3.28: 30146 3.28 - 3.82: 47895 3.82 - 4.36: 57255 4.36 - 4.90: 101486 Nonbonded interactions: 239860 Sorted by model distance: nonbonded pdb=" O MET I 94 " pdb=" OG1 THR I 95 " model vdw 2.208 3.040 nonbonded pdb=" OD2 ASP D 252 " pdb=" OG1 THR E 267 " model vdw 2.226 3.040 nonbonded pdb=" O MET H 94 " pdb=" OG1 THR H 95 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR h 42 " pdb=" O LEU h 152 " model vdw 2.251 3.040 nonbonded pdb=" O SER f 50 " pdb=" OG SER f 50 " model vdw 2.268 3.040 ... (remaining 239855 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.860 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.450 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 32179 Z= 0.113 Angle : 0.539 8.787 43829 Z= 0.299 Chirality : 0.043 0.164 4938 Planarity : 0.004 0.064 5745 Dihedral : 14.450 89.770 11635 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.11 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.12), residues: 4092 helix: 0.34 (0.18), residues: 852 sheet: -0.34 (0.17), residues: 1031 loop : -2.18 (0.11), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 378 TYR 0.027 0.001 TYR H 279 PHE 0.009 0.001 PHE I 219 TRP 0.023 0.001 TRP B 232 HIS 0.002 0.000 HIS f 93 Details of bonding type rmsd covalent geometry : bond 0.00211 (32179) covalent geometry : angle 0.53880 (43829) hydrogen bonds : bond 0.27878 ( 976) hydrogen bonds : angle 7.54517 ( 2490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: D 159 MET cc_start: 0.8812 (ttm) cc_final: 0.8525 (ttt) REVERT: E 101 ASP cc_start: 0.8619 (m-30) cc_final: 0.8358 (m-30) REVERT: E 307 MET cc_start: 0.7926 (tpt) cc_final: 0.6719 (mtt) REVERT: F 94 MET cc_start: 0.8332 (tpt) cc_final: 0.8072 (tpt) REVERT: F 321 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7000 (mt-10) REVERT: H 279 TYR cc_start: 0.8042 (m-80) cc_final: 0.6730 (t80) REVERT: H 382 ILE cc_start: 0.6633 (mt) cc_final: 0.6343 (mt) REVERT: G 279 TYR cc_start: 0.8433 (m-80) cc_final: 0.8175 (m-80) REVERT: J 279 TYR cc_start: 0.8132 (m-80) cc_final: 0.7912 (m-80) REVERT: K 123 GLU cc_start: 0.8243 (tp30) cc_final: 0.7358 (mt-10) REVERT: K 279 TYR cc_start: 0.8322 (m-80) cc_final: 0.7044 (m-10) REVERT: K 382 ILE cc_start: 0.6562 (mt) cc_final: 0.6246 (mt) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1965 time to fit residues: 111.6351 Evaluate side-chains 293 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 ASN g 199 ASN h 38 ASN ** h 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN I 119 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.058825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.049661 restraints weight = 79760.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.051253 restraints weight = 44018.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.052347 restraints weight = 28594.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.053090 restraints weight = 20679.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.053606 restraints weight = 16209.849| |-----------------------------------------------------------------------------| r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32179 Z= 0.207 Angle : 0.612 6.463 43829 Z= 0.336 Chirality : 0.047 0.172 4938 Planarity : 0.004 0.052 5745 Dihedral : 4.883 23.613 4415 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.62 % Favored : 92.08 % Rotamer: Outliers : 0.51 % Allowed : 5.91 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.13), residues: 4092 helix: 1.00 (0.18), residues: 861 sheet: -0.50 (0.16), residues: 1096 loop : -2.30 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 378 TYR 0.026 0.002 TYR K 279 PHE 0.015 0.001 PHE F 190 TRP 0.017 0.001 TRP F 112 HIS 0.004 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00481 (32179) covalent geometry : angle 0.61152 (43829) hydrogen bonds : bond 0.06525 ( 976) hydrogen bonds : angle 5.70126 ( 2490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: B 382 ILE cc_start: 0.6977 (mm) cc_final: 0.6690 (tp) REVERT: C 113 GLU cc_start: 0.5691 (mm-30) cc_final: 0.5453 (mm-30) REVERT: E 101 ASP cc_start: 0.8409 (m-30) cc_final: 0.8179 (m-30) REVERT: E 164 GLU cc_start: 0.4195 (mm-30) cc_final: 0.3568 (mm-30) REVERT: E 307 MET cc_start: 0.7824 (tpt) cc_final: 0.6310 (mpp) REVERT: E 351 GLU cc_start: 0.5056 (mt-10) cc_final: 0.4429 (mt-10) REVERT: F 244 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8307 (ttt-90) REVERT: H 279 TYR cc_start: 0.8115 (m-80) cc_final: 0.6992 (t80) REVERT: H 382 ILE cc_start: 0.7073 (mt) cc_final: 0.6818 (mt) REVERT: G 279 TYR cc_start: 0.8334 (m-80) cc_final: 0.8035 (m-80) REVERT: I 382 ILE cc_start: 0.6982 (mt) cc_final: 0.6765 (mt) REVERT: K 279 TYR cc_start: 0.8341 (m-80) cc_final: 0.7521 (m-10) REVERT: K 382 ILE cc_start: 0.6969 (mt) cc_final: 0.6702 (mt) outliers start: 17 outliers final: 13 residues processed: 293 average time/residue: 0.1979 time to fit residues: 95.6395 Evaluate side-chains 284 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 154 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 114 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 211 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 398 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 190 optimal weight: 0.0170 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN g 199 ASN h 38 ASN h 208 GLN G 119 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.059735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.050592 restraints weight = 79323.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.052191 restraints weight = 43719.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.053278 restraints weight = 28357.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.054038 restraints weight = 20520.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.054571 restraints weight = 16021.854| |-----------------------------------------------------------------------------| r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32179 Z= 0.153 Angle : 0.565 7.209 43829 Z= 0.308 Chirality : 0.046 0.215 4938 Planarity : 0.004 0.049 5745 Dihedral : 4.884 23.579 4415 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.31 % Favored : 92.40 % Rotamer: Outliers : 1.11 % Allowed : 7.92 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.13), residues: 4092 helix: 1.09 (0.18), residues: 863 sheet: -0.56 (0.16), residues: 1090 loop : -2.31 (0.12), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 378 TYR 0.022 0.001 TYR G 279 PHE 0.011 0.001 PHE F 190 TRP 0.015 0.001 TRP F 112 HIS 0.003 0.001 HIS g 90 Details of bonding type rmsd covalent geometry : bond 0.00348 (32179) covalent geometry : angle 0.56451 (43829) hydrogen bonds : bond 0.04832 ( 976) hydrogen bonds : angle 5.20732 ( 2490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 281 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 ILE cc_start: 0.6948 (mm) cc_final: 0.6691 (tp) REVERT: C 113 GLU cc_start: 0.5753 (mm-30) cc_final: 0.5505 (mm-30) REVERT: C 121 ILE cc_start: 0.8474 (pt) cc_final: 0.8179 (tt) REVERT: E 101 ASP cc_start: 0.8410 (m-30) cc_final: 0.8183 (m-30) REVERT: E 164 GLU cc_start: 0.4191 (mm-30) cc_final: 0.3933 (mm-30) REVERT: E 351 GLU cc_start: 0.5451 (mt-10) cc_final: 0.4914 (mt-10) REVERT: F 112 TRP cc_start: 0.8237 (OUTLIER) cc_final: 0.7570 (t60) REVERT: F 244 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8233 (ttt-90) REVERT: H 279 TYR cc_start: 0.8184 (m-80) cc_final: 0.6602 (t80) REVERT: K 382 ILE cc_start: 0.6874 (mt) cc_final: 0.6649 (mt) outliers start: 37 outliers final: 16 residues processed: 303 average time/residue: 0.1846 time to fit residues: 91.6563 Evaluate side-chains 293 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain G residue 380 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 278 optimal weight: 8.9990 chunk 312 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 332 optimal weight: 0.3980 chunk 7 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN g 199 ASN h 38 ASN I 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.058825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.049643 restraints weight = 79078.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.051232 restraints weight = 43696.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.052311 restraints weight = 28390.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.053064 restraints weight = 20606.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.053606 restraints weight = 16112.390| |-----------------------------------------------------------------------------| r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32179 Z= 0.169 Angle : 0.579 8.017 43829 Z= 0.315 Chirality : 0.046 0.235 4938 Planarity : 0.004 0.048 5745 Dihedral : 4.960 23.675 4415 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.04 % Favored : 91.67 % Rotamer: Outliers : 1.26 % Allowed : 9.63 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.13), residues: 4092 helix: 1.10 (0.18), residues: 859 sheet: -0.62 (0.16), residues: 1091 loop : -2.36 (0.11), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 378 TYR 0.020 0.001 TYR H 279 PHE 0.013 0.001 PHE F 190 TRP 0.015 0.001 TRP F 112 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00391 (32179) covalent geometry : angle 0.57853 (43829) hydrogen bonds : bond 0.04779 ( 976) hydrogen bonds : angle 5.08151 ( 2490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 382 ILE cc_start: 0.6905 (mm) cc_final: 0.6698 (tp) REVERT: A 311 GLU cc_start: 0.7831 (mp0) cc_final: 0.7264 (mp0) REVERT: C 113 GLU cc_start: 0.5882 (mm-30) cc_final: 0.5599 (mm-30) REVERT: C 121 ILE cc_start: 0.8414 (pt) cc_final: 0.8149 (tt) REVERT: C 379 TYR cc_start: 0.8759 (m-10) cc_final: 0.8500 (m-10) REVERT: D 113 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: E 164 GLU cc_start: 0.4202 (mm-30) cc_final: 0.3985 (mm-30) REVERT: E 351 GLU cc_start: 0.5535 (mt-10) cc_final: 0.4945 (mt-10) REVERT: F 112 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7787 (t60) REVERT: g 108 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.7615 (t80) REVERT: h 108 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8654 (m-10) outliers start: 42 outliers final: 23 residues processed: 311 average time/residue: 0.1885 time to fit residues: 96.9298 Evaluate side-chains 298 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain K residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 302 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 356 optimal weight: 8.9990 chunk 369 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 352 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN E 181 GLN g 199 ASN h 38 ASN I 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.058255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.049769 restraints weight = 80999.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.051184 restraints weight = 46504.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.052153 restraints weight = 30869.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.052822 restraints weight = 22719.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.053299 restraints weight = 17985.305| |-----------------------------------------------------------------------------| r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32179 Z= 0.197 Angle : 0.603 8.671 43829 Z= 0.329 Chirality : 0.047 0.243 4938 Planarity : 0.004 0.046 5745 Dihedral : 5.150 23.828 4415 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.26 % Favored : 91.45 % Rotamer: Outliers : 1.71 % Allowed : 10.85 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.12), residues: 4092 helix: 1.05 (0.18), residues: 858 sheet: -0.68 (0.16), residues: 1085 loop : -2.41 (0.11), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 378 TYR 0.023 0.001 TYR K 279 PHE 0.014 0.001 PHE F 190 TRP 0.015 0.001 TRP F 112 HIS 0.004 0.001 HIS g 90 Details of bonding type rmsd covalent geometry : bond 0.00464 (32179) covalent geometry : angle 0.60276 (43829) hydrogen bonds : bond 0.05029 ( 976) hydrogen bonds : angle 5.09023 ( 2490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 GLU cc_start: 0.5825 (mm-30) cc_final: 0.5550 (mm-30) REVERT: C 121 ILE cc_start: 0.8484 (pt) cc_final: 0.8233 (tt) REVERT: C 379 TYR cc_start: 0.8852 (m-10) cc_final: 0.8531 (m-10) REVERT: D 67 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: D 113 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: E 164 GLU cc_start: 0.4078 (mm-30) cc_final: 0.3707 (mm-30) REVERT: E 351 GLU cc_start: 0.5682 (mt-10) cc_final: 0.5057 (mt-10) REVERT: F 112 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7746 (t60) REVERT: F 244 ARG cc_start: 0.8437 (ttt90) cc_final: 0.8119 (ttt90) REVERT: g 108 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.7863 (t80) REVERT: h 108 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8656 (m-10) outliers start: 57 outliers final: 32 residues processed: 314 average time/residue: 0.1873 time to fit residues: 97.7378 Evaluate side-chains 304 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 154 THR Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 183 ASN Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 231 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 391 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 400 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 269 optimal weight: 7.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN g 199 ASN h 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.058447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.049995 restraints weight = 80651.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.051411 restraints weight = 46185.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.052392 restraints weight = 30645.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.053055 restraints weight = 22413.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.053520 restraints weight = 17748.119| |-----------------------------------------------------------------------------| r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32179 Z= 0.184 Angle : 0.594 10.238 43829 Z= 0.324 Chirality : 0.047 0.185 4938 Planarity : 0.004 0.045 5745 Dihedral : 5.135 24.164 4415 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.16 % Favored : 91.54 % Rotamer: Outliers : 1.50 % Allowed : 11.51 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.12), residues: 4092 helix: 1.05 (0.18), residues: 859 sheet: -0.73 (0.16), residues: 1091 loop : -2.44 (0.11), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 378 TYR 0.023 0.001 TYR K 279 PHE 0.012 0.001 PHE H 90 TRP 0.022 0.001 TRP I 112 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00432 (32179) covalent geometry : angle 0.59432 (43829) hydrogen bonds : bond 0.04781 ( 976) hydrogen bonds : angle 5.02440 ( 2490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7753 (mp0) cc_final: 0.7139 (mp0) REVERT: C 113 GLU cc_start: 0.5819 (mm-30) cc_final: 0.5550 (mm-30) REVERT: C 121 ILE cc_start: 0.8465 (pt) cc_final: 0.8200 (tt) REVERT: C 379 TYR cc_start: 0.8886 (m-10) cc_final: 0.8538 (m-10) REVERT: D 67 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: D 113 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: E 164 GLU cc_start: 0.4052 (mm-30) cc_final: 0.3650 (mm-30) REVERT: E 351 GLU cc_start: 0.5680 (mt-10) cc_final: 0.5286 (mt-10) REVERT: F 112 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7842 (t60) REVERT: F 244 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8096 (ttt90) REVERT: g 108 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7969 (t80) REVERT: h 108 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8673 (m-10) REVERT: H 113 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: H 382 ILE cc_start: 0.7023 (mt) cc_final: 0.6820 (mt) outliers start: 50 outliers final: 33 residues processed: 306 average time/residue: 0.1912 time to fit residues: 97.7998 Evaluate side-chains 305 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 111 optimal weight: 4.9990 chunk 372 optimal weight: 7.9990 chunk 339 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 284 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 199 ASN h 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.058665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.050184 restraints weight = 80778.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.051601 restraints weight = 46366.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.052594 restraints weight = 30729.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.053260 restraints weight = 22474.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.053729 restraints weight = 17768.590| |-----------------------------------------------------------------------------| r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32179 Z= 0.172 Angle : 0.586 11.085 43829 Z= 0.319 Chirality : 0.046 0.241 4938 Planarity : 0.004 0.044 5745 Dihedral : 5.082 24.378 4415 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.31 % Favored : 91.40 % Rotamer: Outliers : 1.65 % Allowed : 11.75 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.12), residues: 4092 helix: 1.07 (0.18), residues: 859 sheet: -0.76 (0.16), residues: 1097 loop : -2.44 (0.11), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 378 TYR 0.025 0.001 TYR K 279 PHE 0.011 0.001 PHE H 90 TRP 0.016 0.001 TRP I 112 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00400 (32179) covalent geometry : angle 0.58622 (43829) hydrogen bonds : bond 0.04622 ( 976) hydrogen bonds : angle 4.97399 ( 2490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 GLU cc_start: 0.5879 (mm-30) cc_final: 0.5601 (mm-30) REVERT: C 121 ILE cc_start: 0.8453 (pt) cc_final: 0.8190 (tt) REVERT: C 379 TYR cc_start: 0.8887 (m-10) cc_final: 0.8534 (m-10) REVERT: D 67 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: D 113 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: E 164 GLU cc_start: 0.4178 (mm-30) cc_final: 0.3749 (mm-30) REVERT: E 351 GLU cc_start: 0.5693 (mt-10) cc_final: 0.5288 (mt-10) REVERT: F 112 TRP cc_start: 0.8198 (OUTLIER) cc_final: 0.7883 (t60) REVERT: F 244 ARG cc_start: 0.8455 (ttt90) cc_final: 0.8150 (ttt90) REVERT: g 108 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7969 (t80) REVERT: h 108 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8710 (m-10) REVERT: H 113 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: H 382 ILE cc_start: 0.7228 (mt) cc_final: 0.6929 (mt) REVERT: I 310 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8284 (mm110) outliers start: 55 outliers final: 35 residues processed: 309 average time/residue: 0.1851 time to fit residues: 95.5741 Evaluate side-chains 308 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 112 TRP Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 181 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 312 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN g 199 ASN h 38 ASN I 192 ASN J 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.057523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.049024 restraints weight = 81419.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.050430 restraints weight = 46672.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.051397 restraints weight = 31019.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.052070 restraints weight = 22833.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.052525 restraints weight = 18071.018| |-----------------------------------------------------------------------------| r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 32179 Z= 0.218 Angle : 0.627 11.837 43829 Z= 0.342 Chirality : 0.048 0.295 4938 Planarity : 0.004 0.045 5745 Dihedral : 5.275 25.180 4415 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.68 % Favored : 91.03 % Rotamer: Outliers : 1.59 % Allowed : 12.08 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.12), residues: 4092 helix: 1.01 (0.18), residues: 859 sheet: -0.71 (0.16), residues: 1070 loop : -2.47 (0.11), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 172 TYR 0.030 0.002 TYR K 279 PHE 0.013 0.001 PHE H 90 TRP 0.017 0.001 TRP F 112 HIS 0.004 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00521 (32179) covalent geometry : angle 0.62700 (43829) hydrogen bonds : bond 0.05119 ( 976) hydrogen bonds : angle 5.07025 ( 2490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7857 (mp0) cc_final: 0.7142 (mp0) REVERT: C 121 ILE cc_start: 0.8489 (pt) cc_final: 0.8218 (tt) REVERT: C 379 TYR cc_start: 0.8905 (m-10) cc_final: 0.8556 (m-10) REVERT: D 113 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: E 164 GLU cc_start: 0.4023 (mm-30) cc_final: 0.3554 (mm-30) REVERT: E 351 GLU cc_start: 0.5776 (mt-10) cc_final: 0.5389 (mt-10) REVERT: F 112 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.7814 (t60) REVERT: F 244 ARG cc_start: 0.8472 (ttt90) cc_final: 0.8144 (ttt90) REVERT: F 308 LYS cc_start: 0.8074 (tmmt) cc_final: 0.7626 (ttpt) REVERT: g 108 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8164 (t80) REVERT: h 108 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8718 (m-10) REVERT: H 113 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: H 382 ILE cc_start: 0.7155 (mt) cc_final: 0.6890 (mt) REVERT: I 310 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8299 (mm110) outliers start: 53 outliers final: 36 residues processed: 307 average time/residue: 0.1834 time to fit residues: 94.1479 Evaluate side-chains 301 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 154 THR Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 112 TRP Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 340 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 343 optimal weight: 0.0670 chunk 268 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 38 ASN ** h 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.058611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.050150 restraints weight = 80471.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.051551 restraints weight = 46126.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.052524 restraints weight = 30700.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.053206 restraints weight = 22568.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.053687 restraints weight = 17785.043| |-----------------------------------------------------------------------------| r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32179 Z= 0.168 Angle : 0.595 12.652 43829 Z= 0.323 Chirality : 0.046 0.225 4938 Planarity : 0.004 0.044 5745 Dihedral : 5.125 24.553 4415 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.94 % Favored : 91.74 % Rotamer: Outliers : 1.56 % Allowed : 12.08 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.12), residues: 4092 helix: 1.06 (0.18), residues: 859 sheet: -0.73 (0.16), residues: 1071 loop : -2.44 (0.11), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 172 TYR 0.028 0.001 TYR I 279 PHE 0.011 0.001 PHE H 90 TRP 0.023 0.001 TRP I 112 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00390 (32179) covalent geometry : angle 0.59492 (43829) hydrogen bonds : bond 0.04566 ( 976) hydrogen bonds : angle 4.95630 ( 2490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7799 (mp0) cc_final: 0.7066 (mp0) REVERT: C 121 ILE cc_start: 0.8455 (pt) cc_final: 0.8198 (tt) REVERT: C 379 TYR cc_start: 0.8877 (m-10) cc_final: 0.8534 (m-10) REVERT: D 113 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: E 164 GLU cc_start: 0.3955 (mm-30) cc_final: 0.3434 (mm-30) REVERT: E 351 GLU cc_start: 0.5752 (mt-10) cc_final: 0.5373 (mt-10) REVERT: F 112 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.7766 (t60) REVERT: F 244 ARG cc_start: 0.8430 (ttt90) cc_final: 0.8178 (ttt90) REVERT: F 308 LYS cc_start: 0.7909 (tmmt) cc_final: 0.7616 (tmtt) REVERT: g 108 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8244 (t80) REVERT: h 108 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8636 (m-10) REVERT: H 113 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: H 382 ILE cc_start: 0.7087 (mt) cc_final: 0.6801 (mt) REVERT: I 310 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8226 (mm110) REVERT: J 95 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8392 (p) REVERT: K 382 ILE cc_start: 0.7310 (mt) cc_final: 0.6947 (mt) outliers start: 52 outliers final: 36 residues processed: 305 average time/residue: 0.1844 time to fit residues: 93.7383 Evaluate side-chains 306 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 112 TRP Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 137 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 252 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 330 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 38 ASN ** h 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.058030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.049550 restraints weight = 80834.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.050963 restraints weight = 46443.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.051952 restraints weight = 30771.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.052608 restraints weight = 22518.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.053036 restraints weight = 17855.452| |-----------------------------------------------------------------------------| r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 32179 Z= 0.197 Angle : 0.616 13.042 43829 Z= 0.335 Chirality : 0.047 0.256 4938 Planarity : 0.004 0.050 5745 Dihedral : 5.216 24.466 4415 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.65 % Favored : 91.01 % Rotamer: Outliers : 1.53 % Allowed : 12.20 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.12), residues: 4092 helix: 1.03 (0.18), residues: 859 sheet: -0.73 (0.16), residues: 1070 loop : -2.47 (0.11), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.031 0.002 TYR K 279 PHE 0.013 0.001 PHE H 90 TRP 0.023 0.001 TRP I 112 HIS 0.004 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00466 (32179) covalent geometry : angle 0.61556 (43829) hydrogen bonds : bond 0.04878 ( 976) hydrogen bonds : angle 4.99907 ( 2490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7805 (mp0) cc_final: 0.7090 (mp0) REVERT: C 121 ILE cc_start: 0.8471 (pt) cc_final: 0.8203 (tt) REVERT: C 379 TYR cc_start: 0.8875 (m-10) cc_final: 0.8516 (m-10) REVERT: D 113 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: E 164 GLU cc_start: 0.4050 (mm-30) cc_final: 0.3510 (mm-30) REVERT: E 351 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5416 (mt-10) REVERT: F 112 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.7788 (t60) REVERT: F 244 ARG cc_start: 0.8459 (ttt90) cc_final: 0.8189 (ttt90) REVERT: F 308 LYS cc_start: 0.7864 (tmmt) cc_final: 0.7642 (tmtt) REVERT: g 108 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8211 (t80) REVERT: h 108 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8648 (m-10) REVERT: H 113 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: H 382 ILE cc_start: 0.7107 (mt) cc_final: 0.6852 (mt) REVERT: I 310 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8252 (mm110) REVERT: J 95 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8425 (p) REVERT: K 382 ILE cc_start: 0.7300 (mt) cc_final: 0.6930 (mt) outliers start: 51 outliers final: 40 residues processed: 302 average time/residue: 0.1760 time to fit residues: 88.5135 Evaluate side-chains 309 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE Chi-restraints excluded: chain f residue 138 ASP Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 108 TYR Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 208 GLN Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 108 TYR Chi-restraints excluded: chain h residue 176 THR Chi-restraints excluded: chain h residue 190 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 309 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 94 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 112 TRP Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 163 optimal weight: 9.9990 chunk 403 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 94 optimal weight: 0.2980 chunk 338 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 321 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 overall best weight: 7.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 38 ASN h 38 ASN ** h 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.057253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.048757 restraints weight = 81494.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.050163 restraints weight = 46807.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.051125 restraints weight = 31089.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.051801 restraints weight = 22905.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.052272 restraints weight = 18097.431| |-----------------------------------------------------------------------------| r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 32179 Z= 0.231 Angle : 0.645 12.972 43829 Z= 0.352 Chirality : 0.049 0.287 4938 Planarity : 0.004 0.046 5745 Dihedral : 5.390 25.569 4415 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.68 % Favored : 90.96 % Rotamer: Outliers : 1.50 % Allowed : 12.29 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.12), residues: 4092 helix: 0.96 (0.18), residues: 859 sheet: -0.76 (0.16), residues: 1066 loop : -2.50 (0.11), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 172 TYR 0.029 0.002 TYR K 279 PHE 0.014 0.002 PHE H 90 TRP 0.024 0.001 TRP I 112 HIS 0.004 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00553 (32179) covalent geometry : angle 0.64510 (43829) hydrogen bonds : bond 0.05235 ( 976) hydrogen bonds : angle 5.08688 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5247.24 seconds wall clock time: 91 minutes 13.75 seconds (5473.75 seconds total)