Starting phenix.real_space_refine on Fri Jun 27 02:15:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frs_29406/06_2025/8frs_29406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frs_29406/06_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_29406/06_2025/8frs_29406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frs_29406/06_2025/8frs_29406.map" model { file = "/net/cci-nas-00/data/ceres_data/8frs_29406/06_2025/8frs_29406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frs_29406/06_2025/8frs_29406.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.43, per 1000 atoms: 0.59 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: 6.50 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 3.57 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: 9.96 Time building geometry restraints manager: 7.88 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: 0.02 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: 10.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 64.390 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.180 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (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 TRP 0.023 0.001 TRP B 232 HIS 0.002 0.000 HIS f 93 PHE 0.009 0.001 PHE I 219 TYR 0.027 0.001 TYR H 279 ARG 0.004 0.000 ARG I 378 Details of bonding type rmsd hydrogen bonds : bond 0.27878 ( 976) hydrogen bonds : angle 7.54517 ( 2490) covalent geometry : bond 0.00211 (32179) covalent geometry : angle 0.53880 (43829) *********************** 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 : 3.539 Fit side-chains revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7956 (m-30) cc_final: 0.7550 (m-30) REVERT: D 159 MET cc_start: 0.8812 (ttm) cc_final: 0.8527 (ttt) REVERT: E 101 ASP cc_start: 0.8619 (m-30) cc_final: 0.8359 (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: 0.6999 (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: 0.4054 time to fit residues: 231.2195 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 : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 192 optimal weight: 0.4980 chunk 235 optimal weight: 4.9990 chunk 366 optimal weight: 8.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 199 ASN h 38 ASN h 208 GLN 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 = 0.2609 r_free = 0.2609 target = 0.061520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.052680 restraints weight = 77660.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.054248 restraints weight = 43529.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.055327 restraints weight = 28399.987| |-----------------------------------------------------------------------------| r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32179 Z= 0.164 Angle : 0.585 6.254 43829 Z= 0.320 Chirality : 0.046 0.171 4938 Planarity : 0.004 0.050 5745 Dihedral : 4.748 24.075 4415 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.40 % Favored : 92.30 % Rotamer: Outliers : 0.57 % Allowed : 5.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 4092 helix: 0.95 (0.18), residues: 871 sheet: -0.42 (0.16), residues: 1061 loop : -2.28 (0.11), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 112 HIS 0.003 0.001 HIS G 134 PHE 0.012 0.001 PHE F 190 TYR 0.024 0.001 TYR K 279 ARG 0.006 0.000 ARG I 378 Details of bonding type rmsd hydrogen bonds : bond 0.05519 ( 976) hydrogen bonds : angle 5.56992 ( 2490) covalent geometry : bond 0.00374 (32179) covalent geometry : angle 0.58488 (43829) *********************** 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 311 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 292 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 382 ILE cc_start: 0.6986 (mm) cc_final: 0.6705 (tp) REVERT: C 113 GLU cc_start: 0.5641 (mm-30) cc_final: 0.5414 (mm-30) REVERT: E 101 ASP cc_start: 0.8411 (m-30) cc_final: 0.8173 (m-30) REVERT: E 164 GLU cc_start: 0.4055 (mm-30) cc_final: 0.3722 (mm-30) REVERT: E 307 MET cc_start: 0.7792 (tpt) cc_final: 0.6307 (mpp) REVERT: E 351 GLU cc_start: 0.5038 (mt-10) cc_final: 0.4406 (mt-10) REVERT: H 279 TYR cc_start: 0.8063 (m-80) cc_final: 0.7078 (t80) REVERT: H 382 ILE cc_start: 0.7064 (mt) cc_final: 0.6826 (mt) REVERT: G 158 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8279 (ptt) REVERT: G 279 TYR cc_start: 0.8284 (m-80) cc_final: 0.7934 (m-10) REVERT: I 382 ILE cc_start: 0.7098 (mt) cc_final: 0.6860 (mt) REVERT: K 279 TYR cc_start: 0.8335 (m-80) cc_final: 0.7531 (m-10) REVERT: K 382 ILE cc_start: 0.6999 (mt) cc_final: 0.6706 (mt) outliers start: 19 outliers final: 10 residues processed: 301 average time/residue: 0.4328 time to fit residues: 216.0008 Evaluate side-chains 285 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 274 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE 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 259 GLU 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 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 205 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 401 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 346 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 ASN E 181 GLN g 199 ASN h 38 ASN 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 = 0.2536 r_free = 0.2536 target = 0.058040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.048853 restraints weight = 79864.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.050432 restraints weight = 44111.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.051512 restraints weight = 28626.012| |-----------------------------------------------------------------------------| r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 32179 Z= 0.209 Angle : 0.616 7.473 43829 Z= 0.337 Chirality : 0.048 0.260 4938 Planarity : 0.004 0.052 5745 Dihedral : 5.150 24.956 4415 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.06 % Favored : 91.69 % Rotamer: Outliers : 1.11 % Allowed : 7.98 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.12), residues: 4092 helix: 1.02 (0.18), residues: 857 sheet: -0.57 (0.16), residues: 1085 loop : -2.37 (0.11), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.005 0.001 HIS g 90 PHE 0.017 0.001 PHE F 190 TYR 0.026 0.002 TYR G 279 ARG 0.007 0.000 ARG I 378 Details of bonding type rmsd hydrogen bonds : bond 0.05563 ( 976) hydrogen bonds : angle 5.29929 ( 2490) covalent geometry : bond 0.00493 (32179) covalent geometry : angle 0.61598 (43829) *********************** 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 310 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 4.089 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.8367 (ptm) cc_final: 0.8136 (ptm) REVERT: A 352 LYS cc_start: 0.8932 (tttm) cc_final: 0.8689 (ttmm) REVERT: C 121 ILE cc_start: 0.8499 (pt) cc_final: 0.8199 (tt) REVERT: E 164 GLU cc_start: 0.4097 (mm-30) cc_final: 0.3831 (mm-30) REVERT: E 351 GLU cc_start: 0.5499 (mt-10) cc_final: 0.4918 (mt-10) REVERT: F 112 TRP cc_start: 0.8213 (OUTLIER) cc_final: 0.7631 (t60) REVERT: H 382 ILE cc_start: 0.7062 (mt) cc_final: 0.6857 (mt) outliers start: 37 outliers final: 18 residues processed: 297 average time/residue: 0.4112 time to fit residues: 202.8135 Evaluate side-chains 285 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR 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 67 PHE Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain E 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 120 ASP Chi-restraints excluded: chain g residue 129 ILE 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 288 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 202 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 285 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 310 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2540 r_free = 0.2540 target = 0.058360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2349 r_free = 0.2349 target = 0.049923 restraints weight = 80927.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.051334 restraints weight = 46342.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.052299 restraints weight = 30744.246| |-----------------------------------------------------------------------------| r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32179 Z= 0.197 Angle : 0.603 7.918 43829 Z= 0.330 Chirality : 0.047 0.258 4938 Planarity : 0.004 0.048 5745 Dihedral : 5.192 24.024 4415 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.19 % Favored : 91.50 % Rotamer: Outliers : 1.44 % Allowed : 10.19 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.12), residues: 4092 helix: 0.99 (0.18), residues: 859 sheet: -0.67 (0.16), residues: 1085 loop : -2.41 (0.11), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.004 0.001 HIS g 90 PHE 0.014 0.001 PHE F 190 TYR 0.021 0.001 TYR G 279 ARG 0.005 0.000 ARG I 378 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 976) hydrogen bonds : angle 5.15935 ( 2490) covalent geometry : bond 0.00465 (32179) covalent geometry : angle 0.60327 (43829) *********************** 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 320 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7900 (mp0) cc_final: 0.7323 (mp0) REVERT: C 113 GLU cc_start: 0.5813 (mm-30) cc_final: 0.5609 (mm-30) REVERT: C 121 ILE cc_start: 0.8536 (pt) cc_final: 0.8297 (tt) REVERT: C 379 TYR cc_start: 0.8795 (m-10) cc_final: 0.8556 (m-10) REVERT: D 113 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: E 164 GLU cc_start: 0.4023 (mm-30) cc_final: 0.3713 (mm-30) REVERT: E 351 GLU cc_start: 0.5628 (mt-10) cc_final: 0.5035 (mt-10) REVERT: F 112 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7917 (t60) REVERT: g 108 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.7722 (t80) REVERT: h 108 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8658 (m-10) REVERT: H 382 ILE cc_start: 0.7223 (mt) cc_final: 0.6994 (mt) outliers start: 48 outliers final: 28 residues processed: 304 average time/residue: 0.3983 time to fit residues: 202.1800 Evaluate side-chains 295 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 3.520 ------------------------------------------------------------------------------- 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 71 VAL Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU 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 259 GLU Chi-restraints excluded: chain F residue 327 VAL 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 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 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 K residue 129 VAL Chi-restraints excluded: chain K residue 288 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 285 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 368 optimal weight: 20.0000 chunk 394 optimal weight: 4.9990 chunk 217 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 310 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 = 0.2571 r_free = 0.2571 target = 0.059787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.051316 restraints weight = 79908.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.052743 restraints weight = 45804.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.053729 restraints weight = 30316.295| |-----------------------------------------------------------------------------| r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 32179 Z= 0.132 Angle : 0.548 9.457 43829 Z= 0.297 Chirality : 0.045 0.156 4938 Planarity : 0.004 0.044 5745 Dihedral : 4.875 23.092 4415 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.36 % Favored : 92.35 % Rotamer: Outliers : 1.59 % Allowed : 11.21 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 4092 helix: 1.14 (0.18), residues: 862 sheet: -0.72 (0.16), residues: 1108 loop : -2.40 (0.11), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 232 HIS 0.002 0.001 HIS G 134 PHE 0.010 0.001 PHE H 90 TYR 0.020 0.001 TYR K 279 ARG 0.004 0.000 ARG I 378 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 976) hydrogen bonds : angle 4.90646 ( 2490) covalent geometry : bond 0.00291 (32179) covalent geometry : angle 0.54795 (43829) *********************** 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: 53 poor density : 278 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 ILE cc_start: 0.8433 (pt) cc_final: 0.8201 (tt) REVERT: C 379 TYR cc_start: 0.8820 (m-10) cc_final: 0.8574 (m-10) REVERT: D 113 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: E 164 GLU cc_start: 0.3980 (mm-30) cc_final: 0.3669 (mm-30) REVERT: E 351 GLU cc_start: 0.5605 (mt-10) cc_final: 0.4981 (mt-10) REVERT: F 112 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.7645 (t60) REVERT: g 108 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.7861 (t80) REVERT: h 108 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8688 (m-10) REVERT: H 382 ILE cc_start: 0.7092 (mt) cc_final: 0.6859 (mt) REVERT: K 382 ILE cc_start: 0.6886 (mt) cc_final: 0.6646 (mt) outliers start: 53 outliers final: 26 residues processed: 318 average time/residue: 0.4068 time to fit residues: 215.0374 Evaluate side-chains 303 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 273 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 113 GLU 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 E residue 112 TRP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 259 GLU 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 190 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 129 VAL 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 46 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 63 optimal weight: 0.0000 chunk 230 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 78 optimal weight: 0.0270 chunk 325 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 371 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.061565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.053160 restraints weight = 79913.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.054601 restraints weight = 45532.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.055589 restraints weight = 30062.727| |-----------------------------------------------------------------------------| r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32179 Z= 0.113 Angle : 0.531 10.293 43829 Z= 0.285 Chirality : 0.044 0.195 4938 Planarity : 0.003 0.047 5745 Dihedral : 4.583 25.513 4415 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.33 % Favored : 92.33 % Rotamer: Outliers : 1.44 % Allowed : 11.18 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 4092 helix: 1.24 (0.18), residues: 862 sheet: -0.65 (0.16), residues: 1072 loop : -2.33 (0.12), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 112 HIS 0.001 0.000 HIS J 134 PHE 0.008 0.001 PHE C 319 TYR 0.016 0.001 TYR K 279 ARG 0.003 0.000 ARG I 378 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 976) hydrogen bonds : angle 4.66506 ( 2490) covalent geometry : bond 0.00237 (32179) covalent geometry : angle 0.53051 (43829) *********************** 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 335 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7713 (mp0) cc_final: 0.7131 (mp0) REVERT: C 379 TYR cc_start: 0.8829 (m-10) cc_final: 0.8562 (m-10) REVERT: D 113 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: E 164 GLU cc_start: 0.3923 (mm-30) cc_final: 0.3587 (mm-30) REVERT: E 307 MET cc_start: 0.7834 (tpt) cc_final: 0.6348 (mpp) REVERT: E 351 GLU cc_start: 0.5548 (mt-10) cc_final: 0.4917 (mt-10) REVERT: F 112 TRP cc_start: 0.8253 (OUTLIER) cc_final: 0.7863 (t60) REVERT: g 108 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7832 (t80) REVERT: h 108 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8663 (m-10) REVERT: H 113 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: H 382 ILE cc_start: 0.7045 (mt) cc_final: 0.6830 (mt) REVERT: K 382 ILE cc_start: 0.6844 (mt) cc_final: 0.6612 (mt) outliers start: 48 outliers final: 27 residues processed: 318 average time/residue: 0.3783 time to fit residues: 202.3718 Evaluate side-chains 302 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 3.454 ------------------------------------------------------------------------------- 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 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU 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 109 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain f residue 206 ILE 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 190 ILE 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 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 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 391 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 = 0.2577 r_free = 0.2577 target = 0.060059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.051607 restraints weight = 79982.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.053025 restraints weight = 45719.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.054026 restraints weight = 30326.907| |-----------------------------------------------------------------------------| r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32179 Z= 0.145 Angle : 0.559 10.766 43829 Z= 0.301 Chirality : 0.045 0.184 4938 Planarity : 0.004 0.044 5745 Dihedral : 4.713 25.087 4415 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.94 % Favored : 91.74 % Rotamer: Outliers : 1.71 % Allowed : 11.24 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 4092 helix: 1.23 (0.19), residues: 857 sheet: -0.67 (0.16), residues: 1094 loop : -2.41 (0.11), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 112 HIS 0.002 0.001 HIS G 134 PHE 0.010 0.001 PHE F 190 TYR 0.020 0.001 TYR K 279 ARG 0.008 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 976) hydrogen bonds : angle 4.74882 ( 2490) covalent geometry : bond 0.00331 (32179) covalent geometry : angle 0.55896 (43829) *********************** 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 326 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 ILE cc_start: 0.7752 (tp) cc_final: 0.7460 (mm) REVERT: A 311 GLU cc_start: 0.7791 (mp0) cc_final: 0.7191 (mp0) REVERT: C 379 TYR cc_start: 0.8829 (m-10) cc_final: 0.8503 (m-10) REVERT: D 113 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: E 164 GLU cc_start: 0.4164 (mm-30) cc_final: 0.3702 (tp30) REVERT: E 351 GLU cc_start: 0.5604 (mt-10) cc_final: 0.4837 (mt-10) REVERT: F 112 TRP cc_start: 0.8137 (OUTLIER) cc_final: 0.7736 (t60) REVERT: g 108 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.7831 (t80) REVERT: h 108 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8674 (m-10) REVERT: H 307 MET cc_start: 0.7886 (tpp) cc_final: 0.7350 (tpt) REVERT: K 382 ILE cc_start: 0.6946 (mt) cc_final: 0.6705 (mt) outliers start: 57 outliers final: 36 residues processed: 312 average time/residue: 0.3899 time to fit residues: 204.1901 Evaluate side-chains 308 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 3.259 ------------------------------------------------------------------------------- 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 113 GLU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain D residue 113 GLU 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 109 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain f residue 129 ILE 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 190 ILE 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 255 ASP Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain I residue 129 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 397 optimal weight: 1.9990 chunk 299 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 402 optimal weight: 5.9990 chunk 398 optimal weight: 0.0870 chunk 174 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 229 optimal weight: 9.9990 chunk 114 optimal weight: 0.0570 chunk 148 optimal weight: 10.0000 overall best weight: 1.7880 ------------------------------------------------------------------------------- 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 ** h 83 ASN ** 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 = 0.2620 r_free = 0.2620 target = 0.062064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.053646 restraints weight = 79678.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.055090 restraints weight = 45428.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.056084 restraints weight = 29977.660| |-----------------------------------------------------------------------------| r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32179 Z= 0.110 Angle : 0.530 11.555 43829 Z= 0.284 Chirality : 0.044 0.183 4938 Planarity : 0.003 0.041 5745 Dihedral : 4.470 25.163 4415 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.23 % Favored : 92.45 % Rotamer: Outliers : 1.41 % Allowed : 11.54 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 4092 helix: 1.29 (0.19), residues: 857 sheet: -0.63 (0.16), residues: 1052 loop : -2.31 (0.11), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 112 HIS 0.001 0.000 HIS I 134 PHE 0.008 0.001 PHE C 319 TYR 0.017 0.001 TYR G 279 ARG 0.005 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 976) hydrogen bonds : angle 4.56274 ( 2490) covalent geometry : bond 0.00231 (32179) covalent geometry : angle 0.53036 (43829) *********************** 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 329 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 ILE cc_start: 0.7678 (tp) cc_final: 0.7376 (mm) REVERT: A 311 GLU cc_start: 0.7742 (mp0) cc_final: 0.7142 (mp0) REVERT: D 307 MET cc_start: 0.7673 (tpp) cc_final: 0.5939 (mpp) REVERT: E 164 GLU cc_start: 0.4038 (mm-30) cc_final: 0.3519 (mm-30) REVERT: E 307 MET cc_start: 0.7761 (tpt) cc_final: 0.6348 (mpp) REVERT: E 351 GLU cc_start: 0.5526 (mt-10) cc_final: 0.4849 (mt-10) REVERT: F 112 TRP cc_start: 0.8251 (OUTLIER) cc_final: 0.7892 (t60) REVERT: g 108 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7937 (t80) REVERT: h 108 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8651 (m-10) REVERT: K 382 ILE cc_start: 0.6795 (mt) cc_final: 0.6544 (mt) outliers start: 47 outliers final: 35 residues processed: 315 average time/residue: 0.3712 time to fit residues: 195.3939 Evaluate side-chains 305 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 3.181 ------------------------------------------------------------------------------- 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 113 GLU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS 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 109 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain f residue 44 THR 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 190 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 112 TRP 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 294 MET Chi-restraints excluded: chain I residue 129 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 278 optimal weight: 20.0000 chunk 296 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 375 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 402 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 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 = 0.2541 r_free = 0.2541 target = 0.058395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2349 r_free = 0.2349 target = 0.049916 restraints weight = 80648.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.051325 restraints weight = 46289.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.052302 restraints weight = 30747.934| |-----------------------------------------------------------------------------| r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32179 Z= 0.202 Angle : 0.617 11.897 43829 Z= 0.335 Chirality : 0.047 0.226 4938 Planarity : 0.004 0.038 5745 Dihedral : 5.013 24.409 4415 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.38 % Favored : 91.28 % Rotamer: Outliers : 1.59 % Allowed : 11.57 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 4092 helix: 1.15 (0.19), residues: 858 sheet: -0.67 (0.16), residues: 1062 loop : -2.39 (0.11), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 112 HIS 0.004 0.001 HIS g 90 PHE 0.013 0.001 PHE F 190 TYR 0.026 0.002 TYR G 279 ARG 0.005 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 976) hydrogen bonds : angle 4.89081 ( 2490) covalent geometry : bond 0.00480 (32179) covalent geometry : angle 0.61692 (43829) *********************** 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 320 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 382 ILE cc_start: 0.7902 (tp) cc_final: 0.7581 (mm) REVERT: C 121 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8103 (tt) REVERT: E 164 GLU cc_start: 0.3974 (mm-30) cc_final: 0.3352 (mm-30) REVERT: E 351 GLU cc_start: 0.5706 (mt-10) cc_final: 0.5305 (mt-10) REVERT: F 112 TRP cc_start: 0.8144 (OUTLIER) cc_final: 0.7714 (t60) REVERT: g 108 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8011 (t80) REVERT: h 108 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8625 (m-10) REVERT: G 279 TYR cc_start: 0.8244 (m-80) cc_final: 0.7969 (m-80) REVERT: I 382 ILE cc_start: 0.7282 (mt) cc_final: 0.6974 (mt) REVERT: J 279 TYR cc_start: 0.8443 (m-80) cc_final: 0.8169 (m-80) REVERT: K 382 ILE cc_start: 0.7039 (mt) cc_final: 0.6832 (mt) outliers start: 53 outliers final: 38 residues processed: 308 average time/residue: 0.4030 time to fit residues: 207.2114 Evaluate side-chains 302 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 3.803 ------------------------------------------------------------------------------- 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 C residue 112 TRP Chi-restraints excluded: chain C residue 121 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 113 GLU Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE 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 200 LEU Chi-restraints excluded: chain H residue 85 THR 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 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 307 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 219 optimal weight: 0.0050 chunk 328 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 383 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 overall best weight: 3.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.2570 r_free = 0.2570 target = 0.059775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.051341 restraints weight = 79957.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.052766 restraints weight = 45707.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.053746 restraints weight = 30243.843| |-----------------------------------------------------------------------------| r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32179 Z= 0.150 Angle : 0.580 11.521 43829 Z= 0.313 Chirality : 0.046 0.231 4938 Planarity : 0.004 0.042 5745 Dihedral : 4.889 24.082 4415 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.67 % Favored : 91.98 % Rotamer: Outliers : 1.26 % Allowed : 12.02 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 4092 helix: 1.16 (0.19), residues: 857 sheet: -0.68 (0.16), residues: 1079 loop : -2.42 (0.11), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 112 HIS 0.003 0.001 HIS h 93 PHE 0.010 0.001 PHE H 90 TYR 0.022 0.001 TYR G 279 ARG 0.004 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 976) hydrogen bonds : angle 4.79126 ( 2490) covalent geometry : bond 0.00341 (32179) covalent geometry : angle 0.57963 (43829) ********************** 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 309 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 382 ILE cc_start: 0.7931 (tp) cc_final: 0.7519 (mm) REVERT: A 311 GLU cc_start: 0.7789 (mp0) cc_final: 0.7220 (mp0) REVERT: C 121 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8056 (tt) REVERT: E 164 GLU cc_start: 0.4125 (mm-30) cc_final: 0.3552 (mm-30) REVERT: E 351 GLU cc_start: 0.5665 (mt-10) cc_final: 0.4880 (mt-10) REVERT: F 112 TRP cc_start: 0.8125 (OUTLIER) cc_final: 0.7742 (t60) REVERT: g 108 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.7999 (t80) REVERT: h 108 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8628 (m-10) REVERT: K 382 ILE cc_start: 0.6918 (mt) cc_final: 0.6699 (mt) outliers start: 42 outliers final: 37 residues processed: 298 average time/residue: 0.3855 time to fit residues: 192.0865 Evaluate side-chains 304 residues out of total 3335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 3.410 ------------------------------------------------------------------------------- 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 112 TRP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 352 LYS 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 259 GLU Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 129 ILE 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 190 ILE Chi-restraints excluded: chain h residue 200 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 112 TRP 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 112 TRP 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 140 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 354 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 300 optimal weight: 7.9990 chunk 213 optimal weight: 0.4980 chunk 297 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.2577 r_free = 0.2577 target = 0.060140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.051722 restraints weight = 79825.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.053151 restraints weight = 45780.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.054125 restraints weight = 30252.548| |-----------------------------------------------------------------------------| r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32179 Z= 0.143 Angle : 0.572 11.214 43829 Z= 0.308 Chirality : 0.045 0.191 4938 Planarity : 0.004 0.041 5745 Dihedral : 4.814 23.105 4415 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.97 % Favored : 91.67 % Rotamer: Outliers : 1.29 % Allowed : 12.05 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 4092 helix: 1.20 (0.19), residues: 857 sheet: -0.68 (0.16), residues: 1079 loop : -2.41 (0.11), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 112 HIS 0.002 0.001 HIS h 93 PHE 0.010 0.001 PHE f 118 TYR 0.021 0.001 TYR K 279 ARG 0.004 0.000 ARG I 378 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 976) hydrogen bonds : angle 4.73998 ( 2490) covalent geometry : bond 0.00324 (32179) covalent geometry : angle 0.57226 (43829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10100.50 seconds wall clock time: 177 minutes 38.02 seconds (10658.02 seconds total)