Starting phenix.real_space_refine on Sun Aug 24 04:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dws_27758/08_2025/8dws_27758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dws_27758/08_2025/8dws_27758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dws_27758/08_2025/8dws_27758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dws_27758/08_2025/8dws_27758.map" model { file = "/net/cci-nas-00/data/ceres_data/8dws_27758/08_2025/8dws_27758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dws_27758/08_2025/8dws_27758.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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 156 5.16 5 C 10927 2.51 5 N 2874 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17229 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 353, 2780 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 339} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2741 Classifications: {'peptide': 346} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 335} Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2754 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2749 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 347, 2749 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain: "G" Number of atoms: 2737 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 345, 2737 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 9, 'TRANS': 335} Chain: "H" Number of atoms: 2719 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2719 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.67, per 1000 atoms: 0.27 Number of scatterers: 17229 At special positions: 0 Unit cell: (73.929, 145.264, 313.874, 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 156 16.00 O 3272 8.00 N 2874 7.00 C 10927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 361 " - pdb=" SG CYS H 361 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 801.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4198 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 23 sheets defined 47.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 138 through 144 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 185 through 197 removed outlier: 3.706A pdb=" N LEU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.029A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.907A pdb=" N SER A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.810A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 314 through 333 removed outlier: 6.322A pdb=" N SER A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.570A pdb=" N LYS A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.077A pdb=" N VAL A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.794A pdb=" N ASP B 63 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 145 through 148 Processing helix chain 'B' and resid 185 through 197 Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.575A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.750A pdb=" N TYR B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.512A pdb=" N SER B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.315A pdb=" N VAL B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.964A pdb=" N VAL B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.923A pdb=" N SER D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 314 through 328 Processing helix chain 'D' and resid 328 through 334 removed outlier: 3.543A pdb=" N VAL D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.619A pdb=" N LYS D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 removed outlier: 4.109A pdb=" N GLN D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 removed outlier: 4.124A pdb=" N CYS E 44 " --> pdb=" O PHE E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 removed outlier: 3.825A pdb=" N LEU E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 148 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.543A pdb=" N ASP E 153 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.846A pdb=" N HIS E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 259 removed outlier: 4.670A pdb=" N GLU E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 4.113A pdb=" N ALA E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 328 through 333 removed outlier: 3.560A pdb=" N VAL E 332 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 328 through 333' Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.808A pdb=" N LYS E 339 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 359 removed outlier: 3.669A pdb=" N VAL E 349 " --> pdb=" O HIS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.865A pdb=" N ASP F 63 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 81 removed outlier: 3.843A pdb=" N LYS F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 81' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 145 through 148 Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.518A pdb=" N ASP F 153 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 197 removed outlier: 3.958A pdb=" N LEU F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 222 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.534A pdb=" N MET F 228 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 247 through 261 Processing helix chain 'F' and resid 265 through 268 removed outlier: 3.752A pdb=" N LYS F 268 " --> pdb=" O ASN F 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 284 through 295 removed outlier: 3.523A pdb=" N SER F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 314 through 328 Processing helix chain 'F' and resid 328 through 333 Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.548A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 356 removed outlier: 3.613A pdb=" N VAL F 349 " --> pdb=" O HIS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 145 through 148 Processing helix chain 'G' and resid 150 through 154 removed outlier: 3.609A pdb=" N ASP G 153 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 197 removed outlier: 4.006A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 222 removed outlier: 3.846A pdb=" N LEU G 218 " --> pdb=" O HIS G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 230 removed outlier: 3.582A pdb=" N MET G 228 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 removed outlier: 3.807A pdb=" N ASN G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 260 Processing helix chain 'G' and resid 265 through 268 Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 282 through 295 removed outlier: 3.624A pdb=" N SER G 295 " --> pdb=" O ASP G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 314 through 333 removed outlier: 6.230A pdb=" N SER G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP G 331 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 removed outlier: 4.178A pdb=" N LYS G 339 " --> pdb=" O THR G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.900A pdb=" N VAL G 349 " --> pdb=" O HIS G 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 44 removed outlier: 3.579A pdb=" N PHE H 43 " --> pdb=" O ASN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 144 Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 150 through 154 Processing helix chain 'H' and resid 185 through 192 removed outlier: 3.644A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 3.709A pdb=" N ASN H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 222 removed outlier: 4.230A pdb=" N LEU H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.678A pdb=" N GLU H 230 " --> pdb=" O SER H 226 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS H 231 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.927A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 269 through 281 removed outlier: 3.609A pdb=" N LEU H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.504A pdb=" N SER H 295 " --> pdb=" O ASP H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 313 Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 328 through 333 removed outlier: 3.911A pdb=" N LEU H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 345 Processing helix chain 'H' and resid 345 through 358 removed outlier: 4.153A pdb=" N VAL H 349 " --> pdb=" O HIS H 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.660A pdb=" N ILE A 38 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 155 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A 156 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 101 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 104 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 117 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 72 removed outlier: 6.631A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 213 removed outlier: 8.804A pdb=" N ILE A 243 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS A 205 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.647A pdb=" N ILE B 137 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 86 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS B 135 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 213 removed outlier: 3.878A pdb=" N VAL B 241 " --> pdb=" O CYS B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 23 through 25 removed outlier: 6.489A pdb=" N CYS E 23 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 155 " --> pdb=" O ILE G 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 115 through 118 Processing sheet with id=AB1, first strand: chain 'E' and resid 115 through 118 removed outlier: 3.846A pdb=" N LYS E 101 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N CYS F 23 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET E 35 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 66 through 72 removed outlier: 7.132A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS E 68 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N AARG E 70 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER E 85 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 211 through 213 removed outlier: 6.350A pdb=" N CYS E 203 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 28 through 29 removed outlier: 4.024A pdb=" N LYS F 28 " --> pdb=" O GLN F 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN F 165 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 164 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG F 99 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 57 through 59 removed outlier: 4.162A pdb=" N SER F 59 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU F 65 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS F 66 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 91 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N AARG F 70 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE F 137 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU F 86 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS F 135 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU F 88 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE F 133 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 105 Processing sheet with id=AB7, first strand: chain 'F' and resid 205 through 206 Processing sheet with id=AB8, first strand: chain 'G' and resid 28 through 33 removed outlier: 4.372A pdb=" N LYS G 28 " --> pdb=" O GLN G 165 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG G 99 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 100 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 123 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.562A pdb=" N VAL G 71 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS G 66 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 89 " --> pdb=" O CYS G 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N AARG G 70 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 85 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AC2, first strand: chain 'H' and resid 29 through 35 removed outlier: 4.713A pdb=" N PHE H 158 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER H 105 " --> pdb=" O PHE H 158 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE H 102 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLU H 118 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE H 104 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA H 116 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE H 106 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 66 through 72 removed outlier: 7.277A pdb=" N LYS H 66 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN H 72 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER H 85 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 86 " --> pdb=" O PHE H 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AC5, first strand: chain 'H' and resid 205 through 206 697 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5578 1.34 - 1.46: 3961 1.46 - 1.59: 7797 1.59 - 1.71: 0 1.71 - 1.83: 231 Bond restraints: 17567 Sorted by residual: bond pdb=" N SER G 171 " pdb=" CA SER G 171 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.06e+01 bond pdb=" N GLN G 173 " pdb=" CA GLN G 173 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" N ILE G 170 " pdb=" CA ILE G 170 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.35e-02 5.49e+03 9.09e+00 bond pdb=" N GLU E 46 " pdb=" CA GLU E 46 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.36e+00 bond pdb=" N ASP G 166 " pdb=" CA ASP G 166 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.25e-02 6.40e+03 7.90e+00 ... (remaining 17562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 23583 4.09 - 8.18: 104 8.18 - 12.27: 4 12.27 - 16.36: 0 16.36 - 20.45: 1 Bond angle restraints: 23692 Sorted by residual: angle pdb=" C MET B 176 " pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 121.54 141.99 -20.45 1.91e+00 2.74e-01 1.15e+02 angle pdb=" C ASP G 166 " pdb=" CA ASP G 166 " pdb=" CB ASP G 166 " ideal model delta sigma weight residual 109.64 118.86 -9.22 1.77e+00 3.19e-01 2.71e+01 angle pdb=" CA ILE G 170 " pdb=" C ILE G 170 " pdb=" O ILE G 170 " ideal model delta sigma weight residual 121.98 116.42 5.56 1.21e+00 6.83e-01 2.11e+01 angle pdb=" C VAL D 342 " pdb=" N VAL D 343 " pdb=" CA VAL D 343 " ideal model delta sigma weight residual 121.97 130.03 -8.06 1.80e+00 3.09e-01 2.00e+01 angle pdb=" C VAL B 168 " pdb=" N ASN B 169 " pdb=" CA ASN B 169 " ideal model delta sigma weight residual 121.70 129.48 -7.78 1.80e+00 3.09e-01 1.87e+01 ... (remaining 23687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9678 17.97 - 35.94: 834 35.94 - 53.91: 139 53.91 - 71.88: 30 71.88 - 89.85: 18 Dihedral angle restraints: 10699 sinusoidal: 4269 harmonic: 6430 Sorted by residual: dihedral pdb=" CA SER G 171 " pdb=" C SER G 171 " pdb=" N GLY G 172 " pdb=" CA GLY G 172 " ideal model delta harmonic sigma weight residual -180.00 -126.53 -53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA SER G 167 " pdb=" C SER G 167 " pdb=" N VAL G 168 " pdb=" CA VAL G 168 " ideal model delta harmonic sigma weight residual 180.00 138.67 41.33 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA GLN H 360 " pdb=" C GLN H 360 " pdb=" N CYS H 361 " pdb=" CA CYS H 361 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 10696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2498 0.099 - 0.199: 113 0.199 - 0.298: 4 0.298 - 0.397: 2 0.397 - 0.497: 2 Chirality restraints: 2619 Sorted by residual: chirality pdb=" CA ARG E 198 " pdb=" N ARG E 198 " pdb=" C ARG E 198 " pdb=" CB ARG E 198 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA LYS E 47 " pdb=" N LYS E 47 " pdb=" C LYS E 47 " pdb=" CB LYS E 47 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 2616 not shown) Planarity restraints: 3037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 43 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C PHE E 43 " 0.070 2.00e-02 2.50e+03 pdb=" O PHE E 43 " -0.027 2.00e-02 2.50e+03 pdb=" N CYS E 44 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 52 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C ILE E 52 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE E 52 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS E 53 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 169 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C ASN G 169 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN G 169 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE G 170 " 0.016 2.00e-02 2.50e+03 ... (remaining 3034 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 164 2.59 - 3.17: 15273 3.17 - 3.75: 26430 3.75 - 4.32: 34497 4.32 - 4.90: 57045 Nonbonded interactions: 133409 Sorted by model distance: nonbonded pdb=" OG SER G 21 " pdb=" O MET H 35 " model vdw 2.013 3.040 nonbonded pdb=" OG1 THR G 25 " pdb=" O THR H 37 " model vdw 2.061 3.040 nonbonded pdb=" OG SER F 54 " pdb=" O LEU F 69 " model vdw 2.063 3.040 nonbonded pdb=" O LEU E 76 " pdb=" OG SER E 80 " model vdw 2.084 3.040 nonbonded pdb=" O VAL D 332 " pdb=" OG1 THR D 335 " model vdw 2.091 3.040 ... (remaining 133404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) selection = (chain 'B' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'E' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 361)) selection = (chain 'F' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'G' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'H' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.920 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4530 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 : 0.004 0.052 17569 Z= 0.207 Angle : 0.789 20.445 23696 Z= 0.433 Chirality : 0.047 0.497 2619 Planarity : 0.004 0.065 3037 Dihedral : 14.369 89.853 6495 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.16 % Favored : 91.24 % Rotamer: Outliers : 0.32 % Allowed : 0.47 % Favored : 99.21 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.18), residues: 2168 helix: 0.34 (0.18), residues: 826 sheet: -1.48 (0.28), residues: 345 loop : -1.92 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 99 TYR 0.026 0.002 TYR A 259 PHE 0.029 0.002 PHE E 136 TRP 0.025 0.002 TRP F 67 HIS 0.005 0.001 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00435 (17567) covalent geometry : angle 0.78824 (23692) SS BOND : bond 0.00472 ( 2) SS BOND : angle 2.34532 ( 4) hydrogen bonds : bond 0.19643 ( 693) hydrogen bonds : angle 7.53851 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 254 MET cc_start: 0.7340 (ttp) cc_final: 0.7109 (ttm) REVERT: G 353 TYR cc_start: 0.0306 (t80) cc_final: -0.1649 (m-80) REVERT: H 178 MET cc_start: 0.2555 (pmm) cc_final: 0.2133 (pmm) outliers start: 6 outliers final: 1 residues processed: 130 average time/residue: 0.1340 time to fit residues: 27.5097 Evaluate side-chains 99 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.0030 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 40.0000 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 ASN E 326 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN H 39 ASN ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.082432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.051743 restraints weight = 160583.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.051159 restraints weight = 116971.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.051126 restraints weight = 111332.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.050856 restraints weight = 109334.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.051002 restraints weight = 100518.155| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17569 Z= 0.175 Angle : 0.662 9.512 23696 Z= 0.349 Chirality : 0.043 0.171 2619 Planarity : 0.004 0.062 3037 Dihedral : 5.496 55.649 2316 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.61 % Favored : 91.97 % Rotamer: Outliers : 0.37 % Allowed : 6.33 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.18), residues: 2168 helix: 0.81 (0.18), residues: 846 sheet: -1.47 (0.30), residues: 295 loop : -1.84 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 45 TYR 0.033 0.002 TYR H 24 PHE 0.017 0.002 PHE F 257 TRP 0.028 0.002 TRP E 36 HIS 0.004 0.001 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00374 (17567) covalent geometry : angle 0.66186 (23692) SS BOND : bond 0.00313 ( 2) SS BOND : angle 1.78057 ( 4) hydrogen bonds : bond 0.03647 ( 693) hydrogen bonds : angle 5.61721 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.5805 (tmm) cc_final: 0.5429 (tmm) REVERT: B 341 MET cc_start: 0.8979 (tmm) cc_final: 0.8765 (tmm) REVERT: F 176 MET cc_start: 0.7651 (mmt) cc_final: 0.7163 (mpp) REVERT: F 341 MET cc_start: 0.9232 (tmm) cc_final: 0.9029 (tmm) REVERT: G 117 MET cc_start: 0.7861 (ppp) cc_final: 0.7529 (ppp) REVERT: G 173 GLN cc_start: 0.9460 (mp10) cc_final: 0.9191 (tp40) REVERT: G 341 MET cc_start: 0.4521 (tmm) cc_final: 0.4094 (tmm) REVERT: H 48 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8244 (mmp) REVERT: H 176 MET cc_start: 0.4118 (tmm) cc_final: 0.3802 (mmp) REVERT: H 233 MET cc_start: 0.5413 (ppp) cc_final: 0.5187 (ppp) outliers start: 7 outliers final: 2 residues processed: 108 average time/residue: 0.1291 time to fit residues: 22.1996 Evaluate side-chains 99 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain H residue 48 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 160 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 75 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 206 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN H 312 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.078024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.048232 restraints weight = 168880.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.046941 restraints weight = 165895.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046096 restraints weight = 159477.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.046190 restraints weight = 131484.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.046176 restraints weight = 115462.386| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 17569 Z= 0.323 Angle : 0.827 14.862 23696 Z= 0.432 Chirality : 0.046 0.184 2619 Planarity : 0.006 0.080 3037 Dihedral : 5.995 40.917 2316 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.04 % Favored : 90.50 % Rotamer: Outliers : 1.21 % Allowed : 10.81 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.18), residues: 2168 helix: 0.36 (0.18), residues: 850 sheet: -1.46 (0.28), residues: 337 loop : -2.07 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 139 TYR 0.025 0.003 TYR E 280 PHE 0.028 0.003 PHE F 257 TRP 0.028 0.003 TRP E 338 HIS 0.010 0.002 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00679 (17567) covalent geometry : angle 0.82681 (23692) SS BOND : bond 0.00194 ( 2) SS BOND : angle 1.73188 ( 4) hydrogen bonds : bond 0.04283 ( 693) hydrogen bonds : angle 6.07146 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.6258 (ptp) cc_final: 0.5931 (pmm) REVERT: A 233 MET cc_start: 0.6755 (tmm) cc_final: 0.6394 (tmm) REVERT: B 341 MET cc_start: 0.8937 (tmm) cc_final: 0.8646 (tmm) REVERT: E 269 MET cc_start: 0.8314 (ptt) cc_final: 0.7846 (ptt) REVERT: F 176 MET cc_start: 0.7213 (mmt) cc_final: 0.6782 (mpp) REVERT: F 233 MET cc_start: 0.7898 (pmm) cc_final: 0.7674 (pmm) REVERT: G 176 MET cc_start: 0.6774 (ppp) cc_final: 0.6093 (tpp) REVERT: H 83 TYR cc_start: 0.9721 (OUTLIER) cc_final: 0.9466 (t80) REVERT: H 176 MET cc_start: 0.3866 (tmm) cc_final: 0.3625 (mmp) REVERT: H 233 MET cc_start: 0.6154 (ppp) cc_final: 0.5804 (ppp) REVERT: H 255 MET cc_start: 0.8784 (mmm) cc_final: 0.7677 (mmm) REVERT: H 269 MET cc_start: 0.7574 (ppp) cc_final: 0.6648 (ppp) REVERT: H 288 MET cc_start: 0.9582 (ppp) cc_final: 0.9221 (ppp) outliers start: 23 outliers final: 11 residues processed: 111 average time/residue: 0.1226 time to fit residues: 22.0874 Evaluate side-chains 100 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 83 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 110 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.0020 chunk 204 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.080182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.047102 restraints weight = 165154.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.047389 restraints weight = 101524.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.047134 restraints weight = 73906.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.046882 restraints weight = 66425.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.046882 restraints weight = 60976.790| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17569 Z= 0.122 Angle : 0.616 10.450 23696 Z= 0.325 Chirality : 0.042 0.270 2619 Planarity : 0.003 0.067 3037 Dihedral : 5.303 52.668 2316 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.84 % Favored : 91.74 % Rotamer: Outliers : 1.27 % Allowed : 12.76 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.18), residues: 2168 helix: 1.04 (0.18), residues: 851 sheet: -1.55 (0.29), residues: 314 loop : -1.90 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 45 TYR 0.028 0.001 TYR F 83 PHE 0.016 0.001 PHE F 257 TRP 0.020 0.001 TRP E 36 HIS 0.006 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00256 (17567) covalent geometry : angle 0.61644 (23692) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.82586 ( 4) hydrogen bonds : bond 0.02917 ( 693) hydrogen bonds : angle 5.13521 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.6042 (tmm) cc_final: 0.5580 (tmm) REVERT: B 176 MET cc_start: 0.7786 (mpp) cc_final: 0.6717 (tmm) REVERT: B 288 MET cc_start: 0.9281 (mtm) cc_final: 0.8945 (mtm) REVERT: B 341 MET cc_start: 0.9068 (tmm) cc_final: 0.8743 (tmm) REVERT: E 269 MET cc_start: 0.7942 (ptt) cc_final: 0.7673 (pmm) REVERT: F 83 TYR cc_start: 0.9534 (OUTLIER) cc_final: 0.9321 (t80) REVERT: F 176 MET cc_start: 0.6875 (mmt) cc_final: 0.6522 (mpp) REVERT: G 115 LYS cc_start: 0.6147 (OUTLIER) cc_final: 0.5594 (ptpp) REVERT: G 176 MET cc_start: 0.6805 (ppp) cc_final: 0.6032 (tmm) REVERT: H 83 TYR cc_start: 0.9630 (OUTLIER) cc_final: 0.9410 (t80) REVERT: H 254 MET cc_start: 0.9545 (ppp) cc_final: 0.9318 (ppp) REVERT: H 255 MET cc_start: 0.8394 (mmm) cc_final: 0.7903 (mmm) outliers start: 24 outliers final: 6 residues processed: 112 average time/residue: 0.1341 time to fit residues: 24.1140 Evaluate side-chains 103 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 83 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 161 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 46 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.079242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.047888 restraints weight = 164633.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.047893 restraints weight = 118475.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.047502 restraints weight = 107460.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.047352 restraints weight = 97342.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.047382 restraints weight = 91082.491| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17569 Z= 0.159 Angle : 0.634 14.435 23696 Z= 0.329 Chirality : 0.042 0.243 2619 Planarity : 0.003 0.058 3037 Dihedral : 5.208 48.769 2316 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.26 % Favored : 91.33 % Rotamer: Outliers : 1.64 % Allowed : 13.87 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.18), residues: 2168 helix: 1.17 (0.18), residues: 856 sheet: -1.40 (0.28), residues: 329 loop : -1.90 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 121 TYR 0.024 0.001 TYR F 83 PHE 0.020 0.001 PHE F 257 TRP 0.020 0.001 TRP E 36 HIS 0.010 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00337 (17567) covalent geometry : angle 0.63420 (23692) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.57110 ( 4) hydrogen bonds : bond 0.02900 ( 693) hydrogen bonds : angle 5.13224 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.7197 (tmm) cc_final: 0.6656 (tmm) REVERT: B 176 MET cc_start: 0.7892 (mpp) cc_final: 0.6964 (tmm) REVERT: B 288 MET cc_start: 0.9151 (mtm) cc_final: 0.8923 (mtm) REVERT: B 341 MET cc_start: 0.9023 (tmm) cc_final: 0.8730 (tmm) REVERT: F 176 MET cc_start: 0.7173 (mmt) cc_final: 0.6605 (mpp) REVERT: F 269 MET cc_start: 0.6208 (ptm) cc_final: 0.5861 (ptm) REVERT: G 115 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6225 (pttp) REVERT: G 176 MET cc_start: 0.7061 (ppp) cc_final: 0.6504 (tmm) REVERT: H 83 TYR cc_start: 0.9696 (OUTLIER) cc_final: 0.9479 (t80) REVERT: H 176 MET cc_start: 0.4234 (mmp) cc_final: 0.2839 (tmm) REVERT: H 269 MET cc_start: 0.8514 (ppp) cc_final: 0.8288 (ppp) REVERT: H 291 ASP cc_start: 0.9401 (OUTLIER) cc_final: 0.8955 (m-30) REVERT: H 341 MET cc_start: 0.8890 (tmm) cc_final: 0.8559 (tmm) outliers start: 31 outliers final: 14 residues processed: 119 average time/residue: 0.1301 time to fit residues: 25.1179 Evaluate side-chains 109 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 347 HIS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 291 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 140 optimal weight: 0.0970 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.078226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.047531 restraints weight = 165846.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.047017 restraints weight = 123347.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.046928 restraints weight = 113561.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.046614 restraints weight = 112142.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.046885 restraints weight = 102758.147| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17569 Z= 0.196 Angle : 0.680 10.834 23696 Z= 0.353 Chirality : 0.042 0.263 2619 Planarity : 0.004 0.058 3037 Dihedral : 5.345 42.138 2316 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.63 % Favored : 90.96 % Rotamer: Outliers : 1.90 % Allowed : 14.77 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.19), residues: 2168 helix: 1.07 (0.18), residues: 861 sheet: -1.36 (0.28), residues: 343 loop : -1.94 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 284 TYR 0.051 0.002 TYR F 83 PHE 0.025 0.002 PHE F 257 TRP 0.019 0.002 TRP E 36 HIS 0.007 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00413 (17567) covalent geometry : angle 0.68010 (23692) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.59460 ( 4) hydrogen bonds : bond 0.03071 ( 693) hydrogen bonds : angle 5.32425 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9128 (tt) REVERT: A 233 MET cc_start: 0.7455 (tmm) cc_final: 0.7021 (tmm) REVERT: B 176 MET cc_start: 0.7943 (mpp) cc_final: 0.7035 (tmm) REVERT: B 288 MET cc_start: 0.9146 (mtm) cc_final: 0.8924 (mtm) REVERT: B 341 MET cc_start: 0.8921 (tmm) cc_final: 0.8708 (tmm) REVERT: E 198 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7396 (tpm170) REVERT: F 176 MET cc_start: 0.7289 (mmt) cc_final: 0.6757 (mpp) REVERT: G 115 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6493 (ptpp) REVERT: G 176 MET cc_start: 0.6979 (ppp) cc_final: 0.6559 (tmm) REVERT: H 48 MET cc_start: 0.8828 (mmp) cc_final: 0.8492 (mmp) REVERT: H 83 TYR cc_start: 0.9718 (OUTLIER) cc_final: 0.9461 (t80) REVERT: H 233 MET cc_start: 0.5874 (ptm) cc_final: 0.5426 (ppp) REVERT: H 269 MET cc_start: 0.8493 (ppp) cc_final: 0.8267 (ppp) REVERT: H 291 ASP cc_start: 0.9443 (OUTLIER) cc_final: 0.9003 (m-30) outliers start: 36 outliers final: 22 residues processed: 122 average time/residue: 0.1379 time to fit residues: 26.6108 Evaluate side-chains 117 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 291 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 136 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 HIS ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.078952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.047861 restraints weight = 165884.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.048358 restraints weight = 115996.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047870 restraints weight = 91971.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.047974 restraints weight = 91837.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047895 restraints weight = 83139.451| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17569 Z= 0.121 Angle : 0.653 15.932 23696 Z= 0.333 Chirality : 0.042 0.292 2619 Planarity : 0.003 0.058 3037 Dihedral : 5.117 49.051 2316 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.98 % Favored : 91.70 % Rotamer: Outliers : 1.58 % Allowed : 15.56 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.19), residues: 2168 helix: 1.27 (0.18), residues: 858 sheet: -1.32 (0.28), residues: 347 loop : -1.89 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 99 TYR 0.028 0.001 TYR A 83 PHE 0.018 0.001 PHE F 257 TRP 0.026 0.002 TRP H 194 HIS 0.010 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00264 (17567) covalent geometry : angle 0.65286 (23692) SS BOND : bond 0.00212 ( 2) SS BOND : angle 0.53096 ( 4) hydrogen bonds : bond 0.02804 ( 693) hydrogen bonds : angle 5.01730 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9137 (tt) REVERT: A 233 MET cc_start: 0.7488 (tmm) cc_final: 0.7201 (tmm) REVERT: B 176 MET cc_start: 0.7900 (mpp) cc_final: 0.7017 (tmm) REVERT: B 288 MET cc_start: 0.9203 (mtm) cc_final: 0.8879 (mtm) REVERT: B 341 MET cc_start: 0.8961 (tmm) cc_final: 0.8662 (tmm) REVERT: F 176 MET cc_start: 0.7276 (mmt) cc_final: 0.6610 (mpp) REVERT: G 35 MET cc_start: 0.8449 (mmp) cc_final: 0.8106 (mmp) REVERT: G 115 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6602 (ptmt) REVERT: G 176 MET cc_start: 0.6822 (ppp) cc_final: 0.6310 (tmm) REVERT: H 83 TYR cc_start: 0.9659 (OUTLIER) cc_final: 0.9377 (t80) REVERT: H 176 MET cc_start: 0.3983 (mmp) cc_final: 0.2643 (tmm) REVERT: H 233 MET cc_start: 0.5729 (ptm) cc_final: 0.5361 (ppp) REVERT: H 269 MET cc_start: 0.8564 (ppp) cc_final: 0.8269 (ppp) REVERT: H 291 ASP cc_start: 0.9382 (OUTLIER) cc_final: 0.8889 (m-30) REVERT: H 341 MET cc_start: 0.8958 (tmm) cc_final: 0.8588 (tmm) outliers start: 30 outliers final: 19 residues processed: 117 average time/residue: 0.1006 time to fit residues: 19.0509 Evaluate side-chains 113 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 291 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 176 optimal weight: 40.0000 chunk 67 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 50 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 25 optimal weight: 0.0170 overall best weight: 1.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.078980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.047625 restraints weight = 161792.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.048118 restraints weight = 111476.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.047553 restraints weight = 88549.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.047514 restraints weight = 91180.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.047747 restraints weight = 80660.071| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17569 Z= 0.130 Angle : 0.655 13.764 23696 Z= 0.330 Chirality : 0.042 0.296 2619 Planarity : 0.003 0.055 3037 Dihedral : 5.036 47.377 2316 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.16 % Favored : 91.51 % Rotamer: Outliers : 1.74 % Allowed : 15.56 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.19), residues: 2168 helix: 1.30 (0.18), residues: 859 sheet: -1.22 (0.29), residues: 322 loop : -1.86 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 284 TYR 0.018 0.001 TYR A 83 PHE 0.019 0.001 PHE F 257 TRP 0.015 0.001 TRP H 194 HIS 0.010 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00283 (17567) covalent geometry : angle 0.65466 (23692) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.51240 ( 4) hydrogen bonds : bond 0.02755 ( 693) hydrogen bonds : angle 4.98633 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9220 (tt) REVERT: A 233 MET cc_start: 0.7671 (tmm) cc_final: 0.7394 (tmm) REVERT: B 176 MET cc_start: 0.7963 (mpp) cc_final: 0.7185 (tmm) REVERT: B 341 MET cc_start: 0.9229 (tmm) cc_final: 0.8878 (tmm) REVERT: D 345 HIS cc_start: 0.8595 (t-90) cc_final: 0.8367 (t-90) REVERT: E 198 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7650 (tpm170) REVERT: F 176 MET cc_start: 0.7263 (mmt) cc_final: 0.6585 (mpp) REVERT: G 35 MET cc_start: 0.8563 (mmp) cc_final: 0.8247 (mmp) REVERT: G 115 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6233 (ptmt) REVERT: H 83 TYR cc_start: 0.9710 (OUTLIER) cc_final: 0.9466 (t80) REVERT: H 176 MET cc_start: 0.3950 (mmp) cc_final: 0.2587 (tmm) REVERT: H 233 MET cc_start: 0.6124 (ptm) cc_final: 0.5800 (ppp) REVERT: H 291 ASP cc_start: 0.9381 (OUTLIER) cc_final: 0.8896 (m-30) REVERT: H 341 MET cc_start: 0.9025 (tmm) cc_final: 0.8706 (tmm) outliers start: 33 outliers final: 21 residues processed: 115 average time/residue: 0.1162 time to fit residues: 21.7476 Evaluate side-chains 115 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 291 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 2 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 192 optimal weight: 0.0670 chunk 87 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 94 optimal weight: 0.0970 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 7 optimal weight: 0.0000 overall best weight: 1.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS H 312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.078930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.047097 restraints weight = 163122.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.044082 restraints weight = 102312.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.044395 restraints weight = 77699.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.044549 restraints weight = 66578.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.044549 restraints weight = 60987.053| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17569 Z= 0.120 Angle : 0.660 13.210 23696 Z= 0.329 Chirality : 0.041 0.292 2619 Planarity : 0.003 0.056 3037 Dihedral : 4.940 48.205 2316 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.03 % Favored : 91.65 % Rotamer: Outliers : 1.32 % Allowed : 16.30 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.19), residues: 2168 helix: 1.36 (0.19), residues: 854 sheet: -1.12 (0.30), residues: 319 loop : -1.78 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 45 TYR 0.015 0.001 TYR A 83 PHE 0.018 0.001 PHE F 257 TRP 0.012 0.001 TRP E 22 HIS 0.007 0.001 HIS G 345 Details of bonding type rmsd covalent geometry : bond 0.00261 (17567) covalent geometry : angle 0.66008 (23692) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.51065 ( 4) hydrogen bonds : bond 0.02645 ( 693) hydrogen bonds : angle 4.89421 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 233 MET cc_start: 0.6687 (tmm) cc_final: 0.6368 (tmm) REVERT: B 176 MET cc_start: 0.7901 (mpp) cc_final: 0.7138 (tmm) REVERT: B 178 MET cc_start: 0.7581 (tpp) cc_final: 0.6671 (tmm) REVERT: B 288 MET cc_start: 0.9442 (mtp) cc_final: 0.9002 (mtm) REVERT: B 341 MET cc_start: 0.9101 (tmm) cc_final: 0.8764 (tmm) REVERT: F 176 MET cc_start: 0.6741 (mmt) cc_final: 0.6183 (mpp) REVERT: G 115 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.5512 (ptmt) REVERT: G 176 MET cc_start: 0.6523 (tmm) cc_final: 0.5709 (tmm) REVERT: H 48 MET cc_start: 0.8101 (mmp) cc_final: 0.7830 (mmp) REVERT: H 83 TYR cc_start: 0.9369 (OUTLIER) cc_final: 0.9011 (t80) REVERT: H 176 MET cc_start: 0.3802 (mmp) cc_final: 0.2455 (tmm) REVERT: H 291 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.8793 (m-30) REVERT: H 341 MET cc_start: 0.9126 (tmm) cc_final: 0.8806 (tmm) outliers start: 25 outliers final: 18 residues processed: 112 average time/residue: 0.1402 time to fit residues: 24.7294 Evaluate side-chains 112 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 291 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 50.0000 chunk 91 optimal weight: 0.4980 chunk 140 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.079250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.048291 restraints weight = 162757.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.045204 restraints weight = 108824.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.045349 restraints weight = 83392.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.045508 restraints weight = 68087.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.045587 restraints weight = 62391.730| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17569 Z= 0.114 Angle : 0.673 13.142 23696 Z= 0.335 Chirality : 0.041 0.296 2619 Planarity : 0.003 0.055 3037 Dihedral : 4.902 49.020 2316 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.84 % Favored : 91.84 % Rotamer: Outliers : 1.16 % Allowed : 16.40 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.19), residues: 2168 helix: 1.41 (0.19), residues: 852 sheet: -1.01 (0.30), residues: 328 loop : -1.77 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 198 TYR 0.013 0.001 TYR A 83 PHE 0.018 0.001 PHE F 257 TRP 0.013 0.001 TRP A 22 HIS 0.007 0.001 HIS G 345 Details of bonding type rmsd covalent geometry : bond 0.00245 (17567) covalent geometry : angle 0.67304 (23692) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.55116 ( 4) hydrogen bonds : bond 0.02683 ( 693) hydrogen bonds : angle 4.84844 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.6591 (tmm) cc_final: 0.6286 (tmm) REVERT: B 176 MET cc_start: 0.8011 (mpp) cc_final: 0.7272 (tmm) REVERT: B 178 MET cc_start: 0.7544 (tpp) cc_final: 0.6375 (tmm) REVERT: B 288 MET cc_start: 0.9405 (mtp) cc_final: 0.9163 (mtm) REVERT: B 341 MET cc_start: 0.9026 (tmm) cc_final: 0.8706 (tmm) REVERT: F 176 MET cc_start: 0.6722 (mmt) cc_final: 0.6183 (mpp) REVERT: G 35 MET cc_start: 0.8093 (mmp) cc_final: 0.7644 (mmp) REVERT: G 115 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.5382 (ptmt) REVERT: G 176 MET cc_start: 0.6329 (tmm) cc_final: 0.5177 (tmm) REVERT: H 48 MET cc_start: 0.7933 (mmp) cc_final: 0.7686 (mmp) REVERT: H 83 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.9001 (t80) REVERT: H 176 MET cc_start: 0.3053 (mmp) cc_final: 0.1705 (tmm) REVERT: H 288 MET cc_start: 0.9647 (ppp) cc_final: 0.9311 (ppp) REVERT: H 291 ASP cc_start: 0.9336 (OUTLIER) cc_final: 0.8822 (m-30) REVERT: H 341 MET cc_start: 0.9059 (tmm) cc_final: 0.8717 (tmm) outliers start: 22 outliers final: 17 residues processed: 109 average time/residue: 0.1315 time to fit residues: 23.0025 Evaluate side-chains 109 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 291 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 45 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 190 optimal weight: 0.1980 chunk 203 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.078623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.043381 restraints weight = 162994.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.043410 restraints weight = 103129.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.043410 restraints weight = 80914.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.043410 restraints weight = 80914.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.043410 restraints weight = 80914.858| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17569 Z= 0.135 Angle : 0.682 12.260 23696 Z= 0.341 Chirality : 0.041 0.286 2619 Planarity : 0.003 0.054 3037 Dihedral : 4.950 46.791 2316 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.03 % Favored : 91.61 % Rotamer: Outliers : 1.05 % Allowed : 16.61 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.19), residues: 2168 helix: 1.40 (0.19), residues: 852 sheet: -1.02 (0.30), residues: 328 loop : -1.78 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 198 TYR 0.013 0.001 TYR E 280 PHE 0.020 0.001 PHE F 257 TRP 0.015 0.001 TRP B 36 HIS 0.006 0.001 HIS G 345 Details of bonding type rmsd covalent geometry : bond 0.00291 (17567) covalent geometry : angle 0.68243 (23692) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.51036 ( 4) hydrogen bonds : bond 0.02757 ( 693) hydrogen bonds : angle 4.92673 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7163.96 seconds wall clock time: 123 minutes 7.04 seconds (7387.04 seconds total)