Starting phenix.real_space_refine on Tue Aug 26 12:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ouu_70882/08_2025/9ouu_70882.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ouu_70882/08_2025/9ouu_70882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ouu_70882/08_2025/9ouu_70882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ouu_70882/08_2025/9ouu_70882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ouu_70882/08_2025/9ouu_70882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ouu_70882/08_2025/9ouu_70882.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 315 5.16 5 C 22503 2.51 5 N 5899 2.21 5 O 6739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35456 Number of models: 1 Model: "" Number of chains: 15 Chain: "P" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1634 Classifications: {'peptide': 210} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain breaks: 2 Chain: "B" Number of atoms: 2760 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 337} Chain: "D" Number of atoms: 2752 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 348, 2752 Classifications: {'peptide': 348} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 336} Chain: "A" Number of atoms: 2752 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 348, 2752 Classifications: {'peptide': 348} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 336} Chain breaks: 1 Chain: "C" Number of atoms: 2760 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 337} Chain: "F" Number of atoms: 2760 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 10, 'TRANS': 338} Chain: "I" Number of atoms: 1100 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 135, 1100 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 130} Chain: "J" Number of atoms: 2734 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2734 Classifications: {'peptide': 346} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 335} Chain: "E" Number of atoms: 1100 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 135, 1100 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 130} Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 160, 1290 Classifications: {'peptide': 160} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 154} Chain: "H" Number of atoms: 2778 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 352, 2778 Classifications: {'peptide': 352} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 338} Chain: "K" Number of atoms: 2734 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2734 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain: "M" Number of atoms: 2760 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 337} Chain breaks: 1 Chain: "L" Number of atoms: 2778 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 352, 2778 Classifications: {'peptide': 352} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 338} Chain: "N" Number of atoms: 2764 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 350, 2764 Classifications: {'peptide': 350} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 338} Time building chain proxies: 9.46, per 1000 atoms: 0.27 Number of scatterers: 35456 At special positions: 0 Unit cell: (133.182, 154.322, 323.442, 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 315 16.00 O 6739 8.00 N 5899 7.00 C 22503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 361 " - pdb=" SG CYS K 361 " distance=1.98 Simple disulfide: pdb=" SG CYS J 361 " - pdb=" SG CYS M 361 " distance=2.05 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8582 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 35 sheets defined 41.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'P' and resid 185 through 197 Processing helix chain 'P' and resid 214 through 222 removed outlier: 3.617A pdb=" N LEU P 218 " --> pdb=" O HIS P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 229 removed outlier: 3.642A pdb=" N MET P 228 " --> pdb=" O VAL P 224 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE P 229 " --> pdb=" O PHE P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 261 Processing helix chain 'P' and resid 265 through 268 removed outlier: 3.826A pdb=" N LYS P 268 " --> pdb=" O ASN P 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 265 through 268' Processing helix chain 'P' and resid 269 through 280 Processing helix chain 'P' and resid 282 through 295 Processing helix chain 'P' and resid 301 through 312 Processing helix chain 'P' and resid 314 through 328 Processing helix chain 'P' and resid 328 through 333 removed outlier: 3.540A pdb=" N LEU P 333 " --> pdb=" O ALA P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 345 removed outlier: 3.745A pdb=" N VAL P 343 " --> pdb=" O LYS P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 358 removed outlier: 3.801A pdb=" N VAL P 349 " --> pdb=" O HIS P 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.899A pdb=" N LYS B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.737A pdb=" N ASP B 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 Processing helix chain 'B' and resid 214 through 222 removed outlier: 3.787A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 4.028A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 265 through 268 removed outlier: 3.641A pdb=" N LYS B 268 " --> pdb=" O ASN B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.826A pdb=" N SER B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.739A pdb=" N LEU B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.035A pdb=" N LYS B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.551A pdb=" N VAL B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.802A pdb=" N LYS D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 145 through 148 Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 185 through 196 removed outlier: 3.774A pdb=" N LEU D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.626A pdb=" N HIS D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 4.328A pdb=" N GLU D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 removed outlier: 4.216A pdb=" N ALA D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 315 through 328 Processing helix chain 'D' and resid 328 through 333 removed outlier: 4.249A pdb=" N LEU D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.711A pdb=" N LYS D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.721A pdb=" N VAL D 349 " --> pdb=" O HIS D 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.881A pdb=" N LYS A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.558A pdb=" N ASP A 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.935A pdb=" N LEU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.718A pdb=" N HIS A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 4.406A 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 280 removed outlier: 3.838A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.558A pdb=" N VAL A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 333' Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.525A pdb=" N LYS A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.647A pdb=" N VAL A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.874A pdb=" N LYS C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 145 through 148 Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.721A pdb=" N ASP C 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 removed outlier: 3.759A pdb=" N GLY C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 removed outlier: 3.857A pdb=" N LEU C 218 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.976A pdb=" N MET C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 229 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 265 through 268 removed outlier: 3.625A pdb=" N LYS C 268 " --> pdb=" O ASN C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 269 through 281 Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.877A pdb=" N SER C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.980A pdb=" N LEU C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 removed outlier: 4.178A pdb=" N LYS C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 360 removed outlier: 3.593A pdb=" N VAL C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.600A pdb=" N LYS F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) 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: 3.647A pdb=" N ASP F 153 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 197 Processing helix chain 'F' and resid 215 through 222 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.514A pdb=" N MET F 228 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.909A 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: 3.647A 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 281 Processing helix chain 'F' and resid 284 through 295 Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 314 through 333 removed outlier: 3.585A pdb=" N LYS F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP F 331 " --> pdb=" O TYR F 327 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 333 " --> pdb=" O ALA F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.884A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 358 removed outlier: 3.631A pdb=" N VAL F 349 " --> pdb=" O HIS F 345 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 358 " --> pdb=" O ARG F 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 143 Processing helix chain 'I' and resid 150 through 154 removed outlier: 3.701A pdb=" N ASP I 153 " --> pdb=" O LEU I 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 144 Processing helix chain 'J' and resid 150 through 154 removed outlier: 3.705A pdb=" N ASP J 153 " --> pdb=" O LEU J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 192 removed outlier: 3.768A pdb=" N GLU J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 197 removed outlier: 4.103A pdb=" N ASN J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 222 removed outlier: 4.048A pdb=" N LEU J 218 " --> pdb=" O HIS J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 231 removed outlier: 3.838A pdb=" N HIS J 231 " --> pdb=" O ALA J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 261 removed outlier: 3.729A pdb=" N GLU J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 268 No H-bonds generated for 'chain 'J' and resid 266 through 268' Processing helix chain 'J' and resid 269 through 280 Processing helix chain 'J' and resid 282 through 295 removed outlier: 4.023A pdb=" N SER J 295 " --> pdb=" O ASP J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 312 Processing helix chain 'J' and resid 314 through 328 Processing helix chain 'J' and resid 335 through 345 Processing helix chain 'J' and resid 345 through 359 removed outlier: 3.599A pdb=" N VAL J 349 " --> pdb=" O HIS J 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.776A pdb=" N ASP E 153 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 81 removed outlier: 3.822A pdb=" N LYS G 81 " --> pdb=" O GLU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 144 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'H' and resid 77 through 81 removed outlier: 4.062A pdb=" N LYS H 81 " --> pdb=" O GLU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 150 through 154 Processing helix chain 'H' and resid 185 through 197 removed outlier: 4.203A pdb=" N GLY H 192 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU H 195 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 222 removed outlier: 4.040A pdb=" N LEU H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.774A pdb=" N GLU H 230 " --> pdb=" O SER H 226 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS H 231 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 removed outlier: 4.296A pdb=" N SER H 236 " --> pdb=" O GLU H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 4.491A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 270 removed outlier: 3.673A pdb=" N ALA H 270 " --> pdb=" O ASP H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 281 Processing helix chain 'H' and resid 282 through 295 Processing helix chain 'H' and resid 301 through 312 Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 335 through 345 removed outlier: 3.649A pdb=" N LYS H 339 " --> pdb=" O THR H 335 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL H 343 " --> pdb=" O LYS H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 357 Processing helix chain 'K' and resid 77 through 81 removed outlier: 3.697A pdb=" N LYS K 81 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 144 Processing helix chain 'K' and resid 145 through 148 Processing helix chain 'K' and resid 150 through 154 removed outlier: 3.621A pdb=" N ASP K 153 " --> pdb=" O LEU K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 192 removed outlier: 3.779A pdb=" N GLU K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 197 removed outlier: 3.842A pdb=" N ASN K 196 " --> pdb=" O GLY K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 221 removed outlier: 3.878A pdb=" N LEU K 218 " --> pdb=" O HIS K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 231 removed outlier: 3.939A pdb=" N HIS K 231 " --> pdb=" O ALA K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 261 removed outlier: 3.541A pdb=" N GLU K 253 " --> pdb=" O GLU K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 268 No H-bonds generated for 'chain 'K' and resid 266 through 268' Processing helix chain 'K' and resid 269 through 281 Processing helix chain 'K' and resid 282 through 295 removed outlier: 3.973A pdb=" N SER K 295 " --> pdb=" O ASP K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 312 Processing helix chain 'K' and resid 314 through 328 Processing helix chain 'K' and resid 328 through 333 removed outlier: 4.101A pdb=" N LEU K 333 " --> pdb=" O ALA K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 345 Processing helix chain 'K' and resid 345 through 359 Processing helix chain 'M' and resid 139 through 144 Processing helix chain 'M' and resid 150 through 154 removed outlier: 3.725A pdb=" N ASP M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 197 Processing helix chain 'M' and resid 215 through 222 Processing helix chain 'M' and resid 222 through 228 removed outlier: 3.507A pdb=" N MET M 228 " --> pdb=" O VAL M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 247 through 261 Processing helix chain 'M' and resid 265 through 268 removed outlier: 3.674A pdb=" N LYS M 268 " --> pdb=" O ASN M 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 265 through 268' Processing helix chain 'M' and resid 269 through 280 Processing helix chain 'M' and resid 284 through 295 removed outlier: 3.569A pdb=" N SER M 295 " --> pdb=" O ASP M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 312 Processing helix chain 'M' and resid 315 through 328 Processing helix chain 'M' and resid 328 through 333 Processing helix chain 'M' and resid 335 through 345 removed outlier: 3.923A pdb=" N LYS M 339 " --> pdb=" O THR M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 358 removed outlier: 3.624A pdb=" N VAL M 349 " --> pdb=" O HIS M 345 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER M 358 " --> pdb=" O ARG M 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 44 Processing helix chain 'L' and resid 139 through 144 Processing helix chain 'L' and resid 145 through 148 Processing helix chain 'L' and resid 150 through 154 Processing helix chain 'L' and resid 185 through 197 removed outlier: 3.682A pdb=" N TRP L 194 " --> pdb=" O LEU L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 222 removed outlier: 4.282A pdb=" N LEU L 218 " --> pdb=" O HIS L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 231 removed outlier: 3.683A pdb=" N GLU L 230 " --> pdb=" O SER L 226 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS L 231 " --> pdb=" O ALA L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 237 removed outlier: 4.291A pdb=" N SER L 236 " --> pdb=" O GLU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 261 removed outlier: 4.585A pdb=" N GLU L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 268 No H-bonds generated for 'chain 'L' and resid 266 through 268' Processing helix chain 'L' and resid 269 through 280 Processing helix chain 'L' and resid 282 through 295 Processing helix chain 'L' and resid 301 through 312 removed outlier: 3.507A pdb=" N ILE L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 328 Processing helix chain 'L' and resid 335 through 345 removed outlier: 3.685A pdb=" N LYS L 339 " --> pdb=" O THR L 335 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL L 343 " --> pdb=" O LYS L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 360 removed outlier: 4.037A pdb=" N SER L 358 " --> pdb=" O ARG L 354 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA L 359 " --> pdb=" O SER L 355 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN L 360 " --> pdb=" O LEU L 356 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 48 Processing helix chain 'N' and resid 60 through 64 removed outlier: 3.770A pdb=" N ASP N 63 " --> pdb=" O GLY N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 81 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 145 through 148 Processing helix chain 'N' and resid 185 through 197 Processing helix chain 'N' and resid 214 through 222 removed outlier: 3.536A pdb=" N LEU N 218 " --> pdb=" O HIS N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 229 removed outlier: 3.604A pdb=" N MET N 228 " --> pdb=" O VAL N 224 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE N 229 " --> pdb=" O PHE N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 261 Processing helix chain 'N' and resid 265 through 268 removed outlier: 3.802A pdb=" N LYS N 268 " --> pdb=" O ASN N 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 265 through 268' Processing helix chain 'N' and resid 269 through 280 Processing helix chain 'N' and resid 282 through 295 Processing helix chain 'N' and resid 301 through 312 Processing helix chain 'N' and resid 314 through 328 Processing helix chain 'N' and resid 328 through 333 Processing helix chain 'N' and resid 335 through 345 removed outlier: 3.816A pdb=" N VAL N 343 " --> pdb=" O LYS N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 345 through 358 removed outlier: 3.678A pdb=" N VAL N 349 " --> pdb=" O HIS N 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 209 through 213 removed outlier: 4.091A pdb=" N VAL P 241 " --> pdb=" O CYS P 203 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS P 205 " --> pdb=" O VAL P 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 39 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 22 through 39 current: chain 'B' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 113 through 118 current: chain 'A' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 113 through 118 current: chain 'F' and resid 168 through 169 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 169 current: chain 'K' and resid 113 through 118 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.980A pdb=" N LYS B 66 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 84 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS B 135 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 129 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 206 removed outlier: 3.927A pdb=" N CYS B 202 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA B 213 " --> pdb=" O CYS B 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 26 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 168 through 169 current: chain 'C' and resid 113 through 118 Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 38 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 38 current: chain 'D' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 113 through 118 current: chain 'H' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 113 through 118 current: chain 'M' and resid 113 through 118 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 53 removed outlier: 6.617A pdb=" N LYS D 66 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU D 84 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS D 135 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS D 129 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 202 through 206 removed outlier: 3.734A pdb=" N PHE D 211 " --> pdb=" O LEU D 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.553A pdb=" N VAL A 71 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU A 84 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS A 135 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 202 through 206 removed outlier: 3.667A pdb=" N PHE A 211 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 21 through 26 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 169 current: chain 'I' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 113 through 118 current: chain 'J' and resid 113 through 118 Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 53 removed outlier: 6.591A pdb=" N LYS C 66 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU C 84 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS C 135 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 90 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS C 129 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 204 through 205 Processing sheet with id=AB5, first strand: chain 'F' and resid 29 through 39 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 39 current: chain 'F' and resid 113 through 118 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.563A pdb=" N LYS F 66 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU F 84 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS F 135 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU F 90 " --> pdb=" O LYS F 129 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS F 129 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 209 through 210 removed outlier: 5.638A pdb=" N CYS F 205 " --> pdb=" O ILE F 243 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.761A pdb=" N VAL I 71 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS I 66 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS I 129 " --> pdb=" O LEU I 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 52 through 53 removed outlier: 6.678A pdb=" N LYS J 66 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU J 84 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS J 135 " --> pdb=" O LEU J 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 205 through 206 Processing sheet with id=AC2, first strand: chain 'E' and resid 34 through 38 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 34 through 38 current: chain 'E' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 113 through 118 current: chain 'G' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 113 through 118 current: chain 'K' and resid 168 through 169 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 53 removed outlier: 6.619A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER E 85 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 52 through 53 removed outlier: 6.920A pdb=" N LYS G 66 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU G 84 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS G 135 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 52 through 53 removed outlier: 6.621A pdb=" N LYS H 66 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU H 84 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LYS H 135 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS H 129 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 209 through 213 removed outlier: 8.363A pdb=" N ILE H 243 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N CYS H 205 " --> pdb=" O ILE H 243 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 52 through 53 removed outlier: 6.601A pdb=" N LYS K 66 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU K 84 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS K 135 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU K 90 " --> pdb=" O LYS K 129 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS K 129 " --> pdb=" O LEU K 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AC9, first strand: chain 'M' and resid 52 through 53 removed outlier: 3.651A pdb=" N VAL M 71 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS M 66 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU M 84 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS M 135 " --> pdb=" O LEU M 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 209 through 213 removed outlier: 6.296A pdb=" N CYS M 203 " --> pdb=" O VAL M 241 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE M 243 " --> pdb=" O CYS M 203 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N CYS M 205 " --> pdb=" O ILE M 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 29 through 38 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 38 current: chain 'L' and resid 117 through 118 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 66 through 72 removed outlier: 6.481A pdb=" N LYS L 66 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 209 through 213 removed outlier: 8.329A pdb=" N ILE L 243 " --> pdb=" O CYS L 203 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS L 205 " --> pdb=" O ILE L 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 36 through 37 removed outlier: 3.766A pdb=" N TRP N 36 " --> pdb=" O LEU N 157 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 56 through 59 Processing sheet with id=AD7, first strand: chain 'N' and resid 83 through 84 removed outlier: 4.030A pdb=" N ILE N 137 " --> pdb=" O LEU N 84 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 209 through 213 removed outlier: 6.897A pdb=" N CYS N 203 " --> pdb=" O VAL N 241 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE N 243 " --> pdb=" O CYS N 203 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS N 205 " --> pdb=" O ILE N 243 " (cutoff:3.500A) 1226 hydrogen bonds defined for protein. 3471 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: 7.12 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10021 1.33 - 1.46: 8639 1.46 - 1.58: 17031 1.58 - 1.71: 4 1.71 - 1.84: 465 Bond restraints: 36160 Sorted by residual: bond pdb=" CA VAL D 181 " pdb=" C VAL D 181 " ideal model delta sigma weight residual 1.522 1.558 -0.036 7.10e-03 1.98e+04 2.51e+01 bond pdb=" CA ALA N 19 " pdb=" CB ALA N 19 " ideal model delta sigma weight residual 1.534 1.587 -0.053 1.57e-02 4.06e+03 1.16e+01 bond pdb=" CD LYS I 64 " pdb=" CE LYS I 64 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.86e+00 bond pdb=" CG LEU B 364 " pdb=" CD2 LEU B 364 " ideal model delta sigma weight residual 1.521 1.609 -0.088 3.30e-02 9.18e+02 7.07e+00 bond pdb=" N THR N 25 " pdb=" CA THR N 25 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.24e+00 ... (remaining 36155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 47927 2.46 - 4.93: 724 4.93 - 7.39: 79 7.39 - 9.86: 15 9.86 - 12.32: 4 Bond angle restraints: 48749 Sorted by residual: angle pdb=" N GLU N 20 " pdb=" CA GLU N 20 " pdb=" C GLU N 20 " ideal model delta sigma weight residual 111.87 120.29 -8.42 1.41e+00 5.03e-01 3.56e+01 angle pdb=" C ASN J 174 " pdb=" N THR J 175 " pdb=" CA THR J 175 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" N ARG I 45 " pdb=" CA ARG I 45 " pdb=" CB ARG I 45 " ideal model delta sigma weight residual 114.17 107.84 6.33 1.14e+00 7.69e-01 3.08e+01 angle pdb=" C ASN N 169 " pdb=" N ILE N 170 " pdb=" CA ILE N 170 " ideal model delta sigma weight residual 121.97 131.82 -9.85 1.80e+00 3.09e-01 2.99e+01 angle pdb=" N ARG A 198 " pdb=" CA ARG A 198 " pdb=" C ARG A 198 " ideal model delta sigma weight residual 111.30 118.55 -7.25 1.36e+00 5.41e-01 2.84e+01 ... (remaining 48744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 19526 17.68 - 35.36: 1796 35.36 - 53.04: 530 53.04 - 70.72: 106 70.72 - 88.40: 25 Dihedral angle restraints: 21983 sinusoidal: 8825 harmonic: 13158 Sorted by residual: dihedral pdb=" CA THR J 175 " pdb=" C THR J 175 " pdb=" N MET J 176 " pdb=" CA MET J 176 " ideal model delta harmonic sigma weight residual 180.00 134.71 45.29 0 5.00e+00 4.00e-02 8.20e+01 dihedral pdb=" CA THR K 175 " pdb=" C THR K 175 " pdb=" N MET K 176 " pdb=" CA MET K 176 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA ASN M 177 " pdb=" C ASN M 177 " pdb=" N MET M 178 " pdb=" CA MET M 178 " ideal model delta harmonic sigma weight residual 180.00 147.37 32.63 0 5.00e+00 4.00e-02 4.26e+01 ... (remaining 21980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4850 0.081 - 0.162: 482 0.162 - 0.243: 16 0.243 - 0.324: 3 0.324 - 0.405: 1 Chirality restraints: 5352 Sorted by residual: chirality pdb=" CB ILE N 170 " pdb=" CA ILE N 170 " pdb=" CG1 ILE N 170 " pdb=" CG2 ILE N 170 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CG LEU B 193 " pdb=" CB LEU B 193 " pdb=" CD1 LEU B 193 " pdb=" CD2 LEU B 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE A 52 " pdb=" CA ILE A 52 " pdb=" CG1 ILE A 52 " pdb=" CG2 ILE A 52 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5349 not shown) Planarity restraints: 6258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 361 " 0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO F 362 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO F 362 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 362 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 327 " -0.009 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR C 327 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 327 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 327 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 327 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR C 327 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 327 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 327 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS M 361 " -0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO M 362 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO M 362 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 362 " -0.046 5.00e-02 4.00e+02 ... (remaining 6255 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 10 2.44 - 3.06: 21847 3.06 - 3.67: 54370 3.67 - 4.29: 77259 4.29 - 4.90: 125688 Nonbonded interactions: 279174 Sorted by model distance: nonbonded pdb=" SG CYS P 23 " pdb=" N SER L 55 " model vdw 1.825 3.480 nonbonded pdb=" CB CYS P 23 " pdb=" OG SER L 55 " model vdw 1.852 3.440 nonbonded pdb=" CG2 THR P 25 " pdb=" O LYS L 53 " model vdw 2.116 3.460 nonbonded pdb=" OD1 ASN H 177 " pdb=" OD1 ASP N 291 " model vdw 2.139 3.040 nonbonded pdb=" NH2 ARG E 45 " pdb=" NH1 ARG H 124 " model vdw 2.151 3.200 ... (remaining 279169 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 16 through 361) selection = (chain 'B' and resid 16 through 361) selection = (chain 'C' and resid 16 through 361) selection = (chain 'D' and resid 16 through 361) selection = (chain 'F' and resid 16 through 361) selection = (chain 'H' and resid 16 through 361) selection = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 16 through 361) selection = (chain 'M' and resid 16 through 361) selection = (chain 'N' and resid 16 through 361) } ncs_group { reference = chain 'E' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 33.270 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.005 0.088 36162 Z= 0.254 Angle : 0.807 12.321 48753 Z= 0.456 Chirality : 0.048 0.405 5352 Planarity : 0.006 0.111 6258 Dihedral : 15.511 88.396 13395 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.32 % Favored : 94.41 % Rotamer: Outliers : 6.17 % Allowed : 10.80 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.24 (0.12), residues: 4440 helix: 0.03 (0.13), residues: 1481 sheet: -0.22 (0.18), residues: 829 loop : -1.69 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 99 TYR 0.044 0.002 TYR C 327 PHE 0.025 0.002 PHE L 363 TRP 0.028 0.002 TRP J 36 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00523 (36160) covalent geometry : angle 0.80560 (48749) SS BOND : bond 0.03590 ( 2) SS BOND : angle 6.01069 ( 4) hydrogen bonds : bond 0.12571 ( 1226) hydrogen bonds : angle 6.52777 ( 3471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 677 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 255 MET cc_start: 0.8499 (mmm) cc_final: 0.7997 (mmt) REVERT: P 259 TYR cc_start: 0.5902 (m-80) cc_final: 0.5279 (m-80) REVERT: P 288 MET cc_start: 0.9337 (ttm) cc_final: 0.9065 (mmt) REVERT: P 316 GLN cc_start: 0.9232 (mt0) cc_final: 0.8380 (tt0) REVERT: P 342 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8020 (t) REVERT: B 38 ILE cc_start: 0.8266 (mt) cc_final: 0.8015 (pt) REVERT: B 299 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7291 (t) REVERT: B 328 HIS cc_start: 0.7428 (m90) cc_final: 0.6177 (t70) REVERT: D 53 LYS cc_start: 0.5652 (OUTLIER) cc_final: 0.5195 (tttt) REVERT: D 67 TRP cc_start: 0.7637 (m100) cc_final: 0.7380 (m100) REVERT: D 178 MET cc_start: 0.9108 (mtp) cc_final: 0.8781 (mmm) REVERT: D 182 PRO cc_start: 0.8132 (Cg_exo) cc_final: 0.7710 (Cg_endo) REVERT: D 254 MET cc_start: 0.8653 (ttp) cc_final: 0.8367 (ttm) REVERT: D 265 ASN cc_start: 0.8366 (m-40) cc_final: 0.8050 (t0) REVERT: D 288 MET cc_start: 0.8753 (mtp) cc_final: 0.8504 (mtt) REVERT: A 228 MET cc_start: 0.9557 (ttm) cc_final: 0.9044 (ptm) REVERT: A 231 HIS cc_start: 0.7550 (m-70) cc_final: 0.7316 (m-70) REVERT: A 269 MET cc_start: 0.8555 (ptp) cc_final: 0.6957 (ptp) REVERT: A 348 LEU cc_start: 0.9447 (mt) cc_final: 0.9246 (mt) REVERT: A 353 TYR cc_start: 0.8568 (t80) cc_final: 0.8159 (t80) REVERT: C 228 MET cc_start: 0.2513 (pmm) cc_final: 0.1468 (mtp) REVERT: C 231 HIS cc_start: 0.7136 (m170) cc_final: 0.6884 (m90) REVERT: F 107 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.5744 (mt) REVERT: F 117 MET cc_start: 0.7218 (ptp) cc_final: 0.6902 (mpp) REVERT: F 189 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: F 228 MET cc_start: 0.8839 (ptt) cc_final: 0.7642 (ttp) REVERT: F 255 MET cc_start: 0.8023 (mmp) cc_final: 0.7696 (mmp) REVERT: F 272 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8618 (p0) REVERT: F 288 MET cc_start: 0.8987 (mtp) cc_final: 0.8739 (mtp) REVERT: F 299 VAL cc_start: 0.7352 (OUTLIER) cc_final: 0.6829 (m) REVERT: F 360 GLN cc_start: 0.7285 (mt0) cc_final: 0.6922 (tp40) REVERT: I 156 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8188 (p) REVERT: J 178 MET cc_start: 0.8619 (mtp) cc_final: 0.8176 (mmt) REVERT: J 233 MET cc_start: -0.1066 (ppp) cc_final: -0.1273 (tmm) REVERT: E 41 PHE cc_start: 0.8652 (t80) cc_final: 0.8320 (t80) REVERT: E 48 MET cc_start: 0.7132 (tmm) cc_final: 0.6512 (tmm) REVERT: E 117 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7222 (ppp) REVERT: G 77 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7361 (t0) REVERT: G 79 GLU cc_start: 0.8566 (mp0) cc_final: 0.8163 (mp0) REVERT: G 130 ASP cc_start: 0.8159 (p0) cc_final: 0.7738 (p0) REVERT: G 141 PHE cc_start: 0.8850 (t80) cc_final: 0.8446 (t80) REVERT: G 170 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7890 (tp) REVERT: H 104 PHE cc_start: 0.8140 (m-10) cc_final: 0.6440 (m-10) REVERT: H 117 MET cc_start: 0.6238 (ptp) cc_final: 0.5718 (ptm) REVERT: H 134 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8193 (ttpp) REVERT: H 228 MET cc_start: 0.5221 (tmm) cc_final: 0.4311 (mtp) REVERT: H 233 MET cc_start: -0.0374 (ppp) cc_final: -0.1320 (tmm) REVERT: H 288 MET cc_start: 0.8411 (mmp) cc_final: 0.8103 (mtp) REVERT: H 320 GLN cc_start: 0.7951 (tt0) cc_final: 0.7481 (mm110) REVERT: K 85 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8502 (m) REVERT: K 178 MET cc_start: 0.5073 (mpp) cc_final: 0.4870 (mpp) REVERT: K 295 SER cc_start: 0.9550 (m) cc_final: 0.9296 (p) REVERT: K 348 LEU cc_start: 0.9218 (mt) cc_final: 0.8859 (tt) REVERT: K 353 TYR cc_start: 0.8709 (t80) cc_final: 0.8361 (t80) REVERT: M 27 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8216 (mt) REVERT: M 87 TYR cc_start: 0.8691 (m-80) cc_final: 0.8407 (m-10) REVERT: M 159 CYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7475 (p) REVERT: M 272 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8161 (p0) REVERT: M 280 TYR cc_start: 0.8531 (m-80) cc_final: 0.8006 (m-10) REVERT: M 312 HIS cc_start: 0.7771 (m-70) cc_final: 0.7523 (m170) REVERT: M 316 GLN cc_start: 0.8872 (mt0) cc_final: 0.8635 (tt0) REVERT: L 86 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8099 (mt) REVERT: L 228 MET cc_start: 0.4969 (tmm) cc_final: 0.3579 (ppp) REVERT: N 284 ARG cc_start: 0.7085 (ttt-90) cc_final: 0.6551 (ttp80) REVERT: N 312 HIS cc_start: 0.8142 (m90) cc_final: 0.7902 (m90) REVERT: N 345 HIS cc_start: 0.8282 (m90) cc_final: 0.7562 (m-70) outliers start: 241 outliers final: 56 residues processed: 869 average time/residue: 0.2146 time to fit residues: 302.5391 Evaluate side-chains 460 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 388 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 196 ASN P 239 ASN P 312 HIS ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN D 360 GLN A 39 ASN C 26 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN J 72 ASN J 127 GLN J 177 ASN J 326 ASN G 165 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 GLN K 326 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN M 231 HIS ** L 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 HIS N 174 ASN N 196 ASN N 239 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.082666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.064804 restraints weight = 255017.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.065185 restraints weight = 187449.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.065384 restraints weight = 145813.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.065493 restraints weight = 136697.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.065896 restraints weight = 114562.216| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 36162 Z= 0.191 Angle : 0.648 9.482 48753 Z= 0.346 Chirality : 0.044 0.296 5352 Planarity : 0.004 0.094 6258 Dihedral : 5.309 34.820 4746 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.32 % Favored : 94.39 % Rotamer: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.12), residues: 4440 helix: 0.45 (0.13), residues: 1510 sheet: -0.24 (0.18), residues: 827 loop : -1.53 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 45 TYR 0.030 0.002 TYR J 34 PHE 0.022 0.002 PHE D 102 TRP 0.028 0.002 TRP J 36 HIS 0.005 0.001 HIS L 231 Details of bonding type rmsd covalent geometry : bond 0.00416 (36160) covalent geometry : angle 0.64796 (48749) SS BOND : bond 0.01161 ( 2) SS BOND : angle 1.84548 ( 4) hydrogen bonds : bond 0.03530 ( 1226) hydrogen bonds : angle 5.31133 ( 3471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 453 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 255 MET cc_start: 0.8588 (mmm) cc_final: 0.8073 (mmm) REVERT: P 259 TYR cc_start: 0.6308 (m-80) cc_final: 0.5996 (m-80) REVERT: P 273 LEU cc_start: 0.9152 (tp) cc_final: 0.8552 (tp) REVERT: P 286 LYS cc_start: 0.9630 (pttm) cc_final: 0.9402 (pttm) REVERT: P 316 GLN cc_start: 0.9081 (mt0) cc_final: 0.8569 (mt0) REVERT: P 341 MET cc_start: 0.7267 (ppp) cc_final: 0.6985 (ppp) REVERT: D 117 MET cc_start: 0.8164 (pmm) cc_final: 0.7774 (pmm) REVERT: D 193 LEU cc_start: 0.9306 (mm) cc_final: 0.8987 (tp) REVERT: D 265 ASN cc_start: 0.8314 (m-40) cc_final: 0.7931 (t0) REVERT: D 288 MET cc_start: 0.8504 (mtp) cc_final: 0.8243 (mtt) REVERT: A 341 MET cc_start: 0.8779 (tmm) cc_final: 0.8503 (tmm) REVERT: C 228 MET cc_start: 0.3768 (pmm) cc_final: 0.2565 (mtp) REVERT: C 231 HIS cc_start: 0.7074 (m170) cc_final: 0.6855 (m-70) REVERT: F 228 MET cc_start: 0.8566 (ptt) cc_final: 0.8296 (ptm) REVERT: F 289 CYS cc_start: 0.8546 (m) cc_final: 0.8285 (m) REVERT: I 112 GLU cc_start: 0.7766 (mp0) cc_final: 0.7423 (mp0) REVERT: J 178 MET cc_start: 0.8662 (mtp) cc_final: 0.8323 (mmt) REVERT: J 228 MET cc_start: -0.1297 (ptt) cc_final: -0.1607 (ptt) REVERT: E 41 PHE cc_start: 0.8288 (t80) cc_final: 0.8060 (t80) REVERT: G 79 GLU cc_start: 0.8336 (mp0) cc_final: 0.7771 (mp0) REVERT: G 170 ILE cc_start: 0.7849 (pt) cc_final: 0.7635 (tp) REVERT: H 254 MET cc_start: 0.8263 (ttm) cc_final: 0.7863 (ttm) REVERT: H 255 MET cc_start: 0.8995 (mmp) cc_final: 0.8539 (mmm) REVERT: H 320 GLN cc_start: 0.7185 (tt0) cc_final: 0.6951 (mm110) REVERT: H 349 VAL cc_start: 0.8992 (t) cc_final: 0.8709 (t) REVERT: K 295 SER cc_start: 0.9333 (m) cc_final: 0.8928 (p) REVERT: K 353 TYR cc_start: 0.8160 (t80) cc_final: 0.7938 (t80) REVERT: M 35 MET cc_start: 0.7765 (tpp) cc_final: 0.7400 (tpt) REVERT: M 156 THR cc_start: 0.7768 (m) cc_final: 0.7526 (p) REVERT: M 280 TYR cc_start: 0.8350 (m-80) cc_final: 0.8048 (m-80) REVERT: M 312 HIS cc_start: 0.7754 (m-70) cc_final: 0.7524 (m170) REVERT: M 316 GLN cc_start: 0.8902 (mt0) cc_final: 0.8588 (tt0) REVERT: M 353 TYR cc_start: 0.6343 (t80) cc_final: 0.5239 (t80) REVERT: L 308 LEU cc_start: 0.8649 (mt) cc_final: 0.8207 (pp) REVERT: L 348 LEU cc_start: 0.8365 (tt) cc_final: 0.8064 (mt) REVERT: N 312 HIS cc_start: 0.8257 (m90) cc_final: 0.7944 (m90) REVERT: N 316 GLN cc_start: 0.9012 (mp10) cc_final: 0.8485 (tt0) REVERT: N 341 MET cc_start: 0.8700 (tmm) cc_final: 0.8471 (tmm) REVERT: N 345 HIS cc_start: 0.8151 (m90) cc_final: 0.7916 (m-70) outliers start: 3 outliers final: 0 residues processed: 456 average time/residue: 0.2098 time to fit residues: 156.9592 Evaluate side-chains 322 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 415 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 290 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 GLN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN ** N 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.081540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.063585 restraints weight = 255881.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.063902 restraints weight = 192241.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.063997 restraints weight = 155000.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.064382 restraints weight = 123535.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.064514 restraints weight = 107578.969| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36162 Z= 0.165 Angle : 0.597 9.725 48753 Z= 0.320 Chirality : 0.042 0.272 5352 Planarity : 0.004 0.086 6258 Dihedral : 5.109 34.930 4746 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.63 % Favored : 94.08 % Rotamer: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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: -0.77 (0.12), residues: 4440 helix: 0.59 (0.13), residues: 1502 sheet: -0.11 (0.18), residues: 844 loop : -1.50 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 221 TYR 0.029 0.002 TYR E 83 PHE 0.023 0.002 PHE N 225 TRP 0.026 0.002 TRP F 22 HIS 0.007 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00355 (36160) covalent geometry : angle 0.59639 (48749) SS BOND : bond 0.00170 ( 2) SS BOND : angle 1.48595 ( 4) hydrogen bonds : bond 0.03319 ( 1226) hydrogen bonds : angle 5.13465 ( 3471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 409 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 MET cc_start: 0.8193 (ppp) cc_final: 0.7809 (ppp) REVERT: P 255 MET cc_start: 0.8546 (mmm) cc_final: 0.8158 (mmm) REVERT: P 259 TYR cc_start: 0.6068 (m-80) cc_final: 0.5840 (m-80) REVERT: P 286 LYS cc_start: 0.9643 (pttp) cc_final: 0.9413 (pptt) REVERT: P 316 GLN cc_start: 0.9091 (mt0) cc_final: 0.8579 (mt0) REVERT: D 117 MET cc_start: 0.8129 (pmm) cc_final: 0.7702 (pmm) REVERT: D 183 GLU cc_start: 0.7752 (pm20) cc_final: 0.7549 (pm20) REVERT: D 193 LEU cc_start: 0.9406 (mm) cc_final: 0.9040 (tp) REVERT: D 265 ASN cc_start: 0.8337 (m-40) cc_final: 0.7924 (t0) REVERT: D 288 MET cc_start: 0.8407 (mtp) cc_final: 0.8185 (mtt) REVERT: A 48 MET cc_start: 0.6380 (mtp) cc_final: 0.6178 (mtt) REVERT: A 228 MET cc_start: 0.9122 (ttp) cc_final: 0.8593 (ptm) REVERT: A 341 MET cc_start: 0.8901 (tmm) cc_final: 0.8654 (tmm) REVERT: C 48 MET cc_start: 0.6166 (tpp) cc_final: 0.5964 (mmt) REVERT: C 67 TRP cc_start: 0.7708 (m-10) cc_final: 0.7491 (m-10) REVERT: C 178 MET cc_start: 0.1612 (mmp) cc_final: 0.1401 (mmm) REVERT: C 228 MET cc_start: 0.3577 (pmm) cc_final: 0.2290 (mtp) REVERT: C 231 HIS cc_start: 0.7088 (m170) cc_final: 0.6888 (m-70) REVERT: F 228 MET cc_start: 0.8696 (ptt) cc_final: 0.8225 (ptm) REVERT: F 289 CYS cc_start: 0.8620 (m) cc_final: 0.7959 (m) REVERT: I 112 GLU cc_start: 0.7781 (mp0) cc_final: 0.7466 (mp0) REVERT: J 178 MET cc_start: 0.8748 (mtp) cc_final: 0.8390 (mmt) REVERT: G 170 ILE cc_start: 0.8062 (pt) cc_final: 0.7842 (tp) REVERT: H 254 MET cc_start: 0.8354 (ttm) cc_final: 0.8104 (ttm) REVERT: H 255 MET cc_start: 0.9008 (mmp) cc_final: 0.8568 (mmm) REVERT: H 349 VAL cc_start: 0.8861 (t) cc_final: 0.8545 (t) REVERT: K 117 MET cc_start: 0.5894 (mpp) cc_final: 0.5610 (mpp) REVERT: K 353 TYR cc_start: 0.8308 (t80) cc_final: 0.7979 (t80) REVERT: M 35 MET cc_start: 0.7556 (tpp) cc_final: 0.7221 (tpt) REVERT: M 117 MET cc_start: 0.7529 (tpt) cc_final: 0.7111 (tpp) REVERT: M 156 THR cc_start: 0.7962 (m) cc_final: 0.7715 (p) REVERT: M 316 GLN cc_start: 0.8901 (mt0) cc_final: 0.8557 (tt0) REVERT: M 345 HIS cc_start: 0.8779 (m90) cc_final: 0.8486 (m90) REVERT: L 233 MET cc_start: -0.1469 (ppp) cc_final: -0.1790 (ptm) REVERT: L 254 MET cc_start: 0.8788 (ppp) cc_final: 0.8561 (ppp) REVERT: L 308 LEU cc_start: 0.8635 (mt) cc_final: 0.8174 (pp) REVERT: N 228 MET cc_start: 0.8142 (ptt) cc_final: 0.7929 (ppp) REVERT: N 312 HIS cc_start: 0.8296 (m90) cc_final: 0.8004 (m90) REVERT: N 316 GLN cc_start: 0.9284 (mp10) cc_final: 0.8984 (mp10) outliers start: 4 outliers final: 2 residues processed: 413 average time/residue: 0.2176 time to fit residues: 148.8402 Evaluate side-chains 297 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 106 optimal weight: 0.5980 chunk 381 optimal weight: 0.7980 chunk 142 optimal weight: 30.0000 chunk 64 optimal weight: 0.0270 chunk 171 optimal weight: 1.9990 chunk 291 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 439 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 196 ASN ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.081768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.064545 restraints weight = 254146.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.064370 restraints weight = 179654.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.064559 restraints weight = 151412.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.064783 restraints weight = 131642.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.065144 restraints weight = 110765.150| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36162 Z= 0.129 Angle : 0.559 9.269 48753 Z= 0.300 Chirality : 0.042 0.220 5352 Planarity : 0.003 0.084 6258 Dihedral : 4.851 34.000 4746 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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: -0.63 (0.12), residues: 4440 helix: 0.77 (0.13), residues: 1502 sheet: -0.11 (0.18), residues: 878 loop : -1.47 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 99 TYR 0.026 0.001 TYR E 83 PHE 0.031 0.001 PHE D 251 TRP 0.019 0.001 TRP J 36 HIS 0.004 0.001 HIS L 231 Details of bonding type rmsd covalent geometry : bond 0.00277 (36160) covalent geometry : angle 0.55897 (48749) SS BOND : bond 0.00095 ( 2) SS BOND : angle 1.32748 ( 4) hydrogen bonds : bond 0.03059 ( 1226) hydrogen bonds : angle 4.90899 ( 3471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 MET cc_start: 0.8205 (ppp) cc_final: 0.7897 (ppp) REVERT: P 255 MET cc_start: 0.8531 (mmm) cc_final: 0.8155 (mmm) REVERT: P 259 TYR cc_start: 0.5890 (m-80) cc_final: 0.5650 (m-80) REVERT: P 286 LYS cc_start: 0.9675 (pttp) cc_final: 0.9454 (pptt) REVERT: P 288 MET cc_start: 0.8907 (mmp) cc_final: 0.8425 (mmp) REVERT: P 316 GLN cc_start: 0.9125 (mt0) cc_final: 0.8576 (mt0) REVERT: B 328 HIS cc_start: 0.7586 (m90) cc_final: 0.6542 (t70) REVERT: D 117 MET cc_start: 0.8102 (pmm) cc_final: 0.7568 (pmm) REVERT: D 182 PRO cc_start: 0.8527 (Cg_exo) cc_final: 0.7552 (Cg_endo) REVERT: D 185 ARG cc_start: 0.8963 (mpp80) cc_final: 0.8670 (mpp80) REVERT: D 193 LEU cc_start: 0.9555 (mm) cc_final: 0.9228 (tp) REVERT: D 265 ASN cc_start: 0.8420 (m-40) cc_final: 0.7973 (t0) REVERT: D 288 MET cc_start: 0.8425 (mtp) cc_final: 0.8177 (mtt) REVERT: A 198 ARG cc_start: 0.6095 (tpt90) cc_final: 0.4800 (mmm160) REVERT: A 228 MET cc_start: 0.9237 (ttp) cc_final: 0.8615 (ptm) REVERT: A 341 MET cc_start: 0.9212 (tmm) cc_final: 0.8858 (tmm) REVERT: C 48 MET cc_start: 0.6389 (tpp) cc_final: 0.6173 (mmt) REVERT: C 67 TRP cc_start: 0.8111 (m-10) cc_final: 0.7851 (m-10) REVERT: C 176 MET cc_start: 0.5990 (mpp) cc_final: 0.5603 (mpp) REVERT: C 228 MET cc_start: 0.3519 (pmm) cc_final: 0.2194 (mtp) REVERT: F 228 MET cc_start: 0.8840 (ptt) cc_final: 0.8413 (ptm) REVERT: F 269 MET cc_start: 0.7573 (ptm) cc_final: 0.6342 (ttp) REVERT: F 289 CYS cc_start: 0.8846 (m) cc_final: 0.8367 (m) REVERT: I 112 GLU cc_start: 0.7877 (mp0) cc_final: 0.7552 (mp0) REVERT: J 35 MET cc_start: 0.8796 (tpp) cc_final: 0.8415 (tpp) REVERT: J 178 MET cc_start: 0.8728 (mtp) cc_final: 0.8362 (mmt) REVERT: G 35 MET cc_start: 0.8482 (mmm) cc_final: 0.8233 (mmm) REVERT: H 254 MET cc_start: 0.8157 (ttm) cc_final: 0.7932 (ttm) REVERT: H 255 MET cc_start: 0.9035 (mmp) cc_final: 0.8547 (mmm) REVERT: K 142 LEU cc_start: 0.8833 (tp) cc_final: 0.8574 (mt) REVERT: K 353 TYR cc_start: 0.8640 (t80) cc_final: 0.8184 (t80) REVERT: M 35 MET cc_start: 0.7955 (tpp) cc_final: 0.7491 (tpt) REVERT: M 156 THR cc_start: 0.8314 (m) cc_final: 0.8011 (p) REVERT: M 280 TYR cc_start: 0.8774 (m-10) cc_final: 0.8530 (m-80) REVERT: M 312 HIS cc_start: 0.7819 (m170) cc_final: 0.7313 (m170) REVERT: M 316 GLN cc_start: 0.8910 (mt0) cc_final: 0.8566 (tt0) REVERT: M 345 HIS cc_start: 0.8801 (m90) cc_final: 0.8467 (m90) REVERT: L 175 THR cc_start: 0.8095 (t) cc_final: 0.7371 (t) REVERT: L 185 ARG cc_start: 0.9362 (tpp-160) cc_final: 0.9146 (tpp80) REVERT: L 231 HIS cc_start: 0.8662 (p90) cc_final: 0.8367 (p90) REVERT: L 254 MET cc_start: 0.8779 (ppp) cc_final: 0.8153 (ppp) REVERT: L 255 MET cc_start: 0.8752 (mmp) cc_final: 0.8329 (mmt) REVERT: L 308 LEU cc_start: 0.8624 (mt) cc_final: 0.8136 (pp) REVERT: L 341 MET cc_start: 0.6691 (tmm) cc_final: 0.6473 (tmm) REVERT: L 348 LEU cc_start: 0.8590 (tt) cc_final: 0.8118 (mt) REVERT: N 176 MET cc_start: 0.7579 (tmm) cc_final: 0.7344 (tmm) REVERT: N 228 MET cc_start: 0.8180 (ptt) cc_final: 0.7970 (ppp) REVERT: N 312 HIS cc_start: 0.8361 (m90) cc_final: 0.8027 (m90) REVERT: N 316 GLN cc_start: 0.9306 (mp10) cc_final: 0.8993 (tt0) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.2051 time to fit residues: 134.3804 Evaluate side-chains 300 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 230 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 312 HIS B 127 GLN B 196 ASN ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 328 HIS A 360 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN C 231 HIS ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 GLN ** L 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 345 HIS ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.075521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.057497 restraints weight = 257494.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.057376 restraints weight = 172959.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.057752 restraints weight = 142885.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.057822 restraints weight = 123239.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.058007 restraints weight = 117325.606| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 36162 Z= 0.349 Angle : 0.858 12.340 48753 Z= 0.457 Chirality : 0.049 0.326 5352 Planarity : 0.006 0.111 6258 Dihedral : 6.267 33.674 4746 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.32 % Favored : 92.43 % Rotamer: Outliers : 0.10 % Allowed : 4.91 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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: -1.43 (0.12), residues: 4440 helix: -0.02 (0.13), residues: 1501 sheet: -0.57 (0.18), residues: 866 loop : -1.80 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 124 TYR 0.040 0.003 TYR G 34 PHE 0.045 0.004 PHE I 32 TRP 0.054 0.003 TRP J 36 HIS 0.013 0.002 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00749 (36160) covalent geometry : angle 0.85797 (48749) SS BOND : bond 0.00458 ( 2) SS BOND : angle 2.56177 ( 4) hydrogen bonds : bond 0.04724 ( 1226) hydrogen bonds : angle 5.99087 ( 3471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 329 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 255 MET cc_start: 0.8783 (mmm) cc_final: 0.8532 (mmm) REVERT: P 284 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7700 (ttp80) REVERT: P 286 LYS cc_start: 0.9714 (pttp) cc_final: 0.9468 (pptt) REVERT: P 288 MET cc_start: 0.8934 (mmp) cc_final: 0.8592 (mmp) REVERT: P 316 GLN cc_start: 0.9207 (mt0) cc_final: 0.8832 (mt0) REVERT: B 269 MET cc_start: 0.9254 (mpp) cc_final: 0.9024 (mpp) REVERT: D 34 TYR cc_start: 0.7450 (t80) cc_final: 0.6953 (t80) REVERT: D 117 MET cc_start: 0.8246 (pmm) cc_final: 0.7762 (pmm) REVERT: D 288 MET cc_start: 0.8446 (mtp) cc_final: 0.8245 (mtt) REVERT: A 341 MET cc_start: 0.9174 (tmm) cc_final: 0.8849 (tmm) REVERT: C 176 MET cc_start: 0.6245 (mpp) cc_final: 0.5783 (mpp) REVERT: C 228 MET cc_start: 0.2743 (pmm) cc_final: 0.1203 (mmm) REVERT: F 228 MET cc_start: 0.8444 (ptt) cc_final: 0.7970 (ptm) REVERT: F 289 CYS cc_start: 0.8748 (m) cc_final: 0.8392 (m) REVERT: I 112 GLU cc_start: 0.8077 (mp0) cc_final: 0.7736 (mp0) REVERT: J 117 MET cc_start: 0.8023 (ptp) cc_final: 0.7557 (ptp) REVERT: J 178 MET cc_start: 0.8657 (mtp) cc_final: 0.8322 (mmt) REVERT: J 228 MET cc_start: -0.1472 (ptt) cc_final: -0.1924 (ptt) REVERT: H 228 MET cc_start: 0.5691 (ppp) cc_final: 0.5228 (ptm) REVERT: H 254 MET cc_start: 0.8214 (ttm) cc_final: 0.7927 (ttm) REVERT: H 255 MET cc_start: 0.9124 (mmp) cc_final: 0.8570 (mmm) REVERT: M 87 TYR cc_start: 0.8427 (m-10) cc_final: 0.8039 (m-10) REVERT: M 312 HIS cc_start: 0.7984 (m170) cc_final: 0.7439 (m170) REVERT: M 316 GLN cc_start: 0.8908 (mt0) cc_final: 0.8392 (tt0) REVERT: M 345 HIS cc_start: 0.8581 (m90) cc_final: 0.8330 (m90) REVERT: L 231 HIS cc_start: 0.8820 (p90) cc_final: 0.8595 (p90) REVERT: L 254 MET cc_start: 0.8873 (ppp) cc_final: 0.8299 (ppp) REVERT: L 255 MET cc_start: 0.9046 (mmp) cc_final: 0.8505 (mmm) REVERT: L 269 MET cc_start: 0.8633 (tmm) cc_final: 0.8309 (tmm) REVERT: L 348 LEU cc_start: 0.8600 (tt) cc_final: 0.8191 (mt) REVERT: N 312 HIS cc_start: 0.8336 (m90) cc_final: 0.7971 (m90) outliers start: 4 outliers final: 1 residues processed: 333 average time/residue: 0.2091 time to fit residues: 115.3937 Evaluate side-chains 260 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 57 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 230 optimal weight: 30.0000 chunk 133 optimal weight: 0.9990 chunk 72 optimal weight: 0.0050 chunk 159 optimal weight: 0.5980 chunk 269 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 385 optimal weight: 5.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN F 196 ASN G 165 GLN H 120 GLN H 265 ASN M 127 GLN ** L 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.079845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.061665 restraints weight = 253940.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.062314 restraints weight = 189904.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.062491 restraints weight = 138685.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.062784 restraints weight = 124720.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.062845 restraints weight = 113165.728| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36162 Z= 0.120 Angle : 0.609 9.500 48753 Z= 0.323 Chirality : 0.044 0.388 5352 Planarity : 0.004 0.089 6258 Dihedral : 5.223 28.145 4746 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.99 % Favored : 93.83 % Rotamer: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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 (0.12), residues: 4440 helix: 0.59 (0.13), residues: 1517 sheet: -0.42 (0.18), residues: 820 loop : -1.62 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 99 TYR 0.021 0.001 TYR E 83 PHE 0.020 0.001 PHE H 363 TRP 0.018 0.001 TRP K 36 HIS 0.003 0.001 HIS N 231 Details of bonding type rmsd covalent geometry : bond 0.00255 (36160) covalent geometry : angle 0.60913 (48749) SS BOND : bond 0.01183 ( 2) SS BOND : angle 1.25027 ( 4) hydrogen bonds : bond 0.03246 ( 1226) hydrogen bonds : angle 5.08275 ( 3471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 MET cc_start: 0.8231 (ppp) cc_final: 0.7930 (ppp) REVERT: P 255 MET cc_start: 0.8576 (mmm) cc_final: 0.7987 (mmm) REVERT: P 259 TYR cc_start: 0.5855 (m-80) cc_final: 0.5021 (m-80) REVERT: P 284 ARG cc_start: 0.8027 (ttt-90) cc_final: 0.7541 (ttp80) REVERT: P 288 MET cc_start: 0.8804 (mmp) cc_final: 0.8426 (mmp) REVERT: P 316 GLN cc_start: 0.8993 (mt0) cc_final: 0.8477 (mt0) REVERT: P 341 MET cc_start: 0.8013 (ppp) cc_final: 0.7790 (ppp) REVERT: B 269 MET cc_start: 0.9399 (mpp) cc_final: 0.9146 (mpp) REVERT: B 341 MET cc_start: 0.8294 (tmm) cc_final: 0.8056 (tmm) REVERT: D 117 MET cc_start: 0.7983 (pmm) cc_final: 0.7330 (pmm) REVERT: D 245 ASP cc_start: 0.8364 (m-30) cc_final: 0.8084 (t0) REVERT: D 251 PHE cc_start: 0.9178 (t80) cc_final: 0.8874 (t80) REVERT: D 255 MET cc_start: 0.9499 (ptp) cc_final: 0.9124 (tmm) REVERT: D 288 MET cc_start: 0.8489 (mtp) cc_final: 0.8237 (mtt) REVERT: A 48 MET cc_start: 0.6125 (mtt) cc_final: 0.5750 (mtt) REVERT: A 341 MET cc_start: 0.9233 (tmm) cc_final: 0.8743 (tmm) REVERT: C 176 MET cc_start: 0.6841 (mpp) cc_final: 0.6168 (mpp) REVERT: C 228 MET cc_start: 0.2976 (pmm) cc_final: 0.1687 (mmm) REVERT: F 65 LEU cc_start: 0.9006 (mm) cc_final: 0.8488 (pt) REVERT: F 123 TYR cc_start: 0.8049 (m-80) cc_final: 0.7799 (m-80) REVERT: F 166 ASP cc_start: 0.7374 (p0) cc_final: 0.6959 (p0) REVERT: F 228 MET cc_start: 0.8488 (ptt) cc_final: 0.7968 (ptm) REVERT: F 269 MET cc_start: 0.7683 (ptm) cc_final: 0.6461 (ttp) REVERT: I 112 GLU cc_start: 0.8072 (mp0) cc_final: 0.7747 (mp0) REVERT: J 35 MET cc_start: 0.8815 (tpp) cc_final: 0.8449 (tpp) REVERT: J 178 MET cc_start: 0.8740 (mtp) cc_final: 0.8453 (mmt) REVERT: J 228 MET cc_start: -0.1528 (ptt) cc_final: -0.1877 (ptt) REVERT: G 41 PHE cc_start: 0.8669 (t80) cc_final: 0.8379 (t80) REVERT: H 84 LEU cc_start: 0.8655 (mp) cc_final: 0.8404 (tp) REVERT: H 156 THR cc_start: 0.9043 (m) cc_final: 0.8753 (p) REVERT: H 255 MET cc_start: 0.9065 (mmp) cc_final: 0.8641 (mtm) REVERT: K 117 MET cc_start: 0.5066 (mpp) cc_final: 0.4857 (mpp) REVERT: K 348 LEU cc_start: 0.9173 (tt) cc_final: 0.8876 (tt) REVERT: K 353 TYR cc_start: 0.8525 (t80) cc_final: 0.8275 (t80) REVERT: M 87 TYR cc_start: 0.8380 (m-10) cc_final: 0.8099 (m-80) REVERT: M 228 MET cc_start: 0.8085 (tpp) cc_final: 0.7690 (tpp) REVERT: M 280 TYR cc_start: 0.8802 (m-10) cc_final: 0.8464 (m-80) REVERT: M 312 HIS cc_start: 0.7794 (m170) cc_final: 0.7263 (m170) REVERT: M 345 HIS cc_start: 0.8850 (m90) cc_final: 0.8465 (m90) REVERT: L 228 MET cc_start: 0.4514 (ppp) cc_final: 0.3873 (ppp) REVERT: L 231 HIS cc_start: 0.8788 (p90) cc_final: 0.8576 (p90) REVERT: L 254 MET cc_start: 0.8880 (ppp) cc_final: 0.8390 (ppp) REVERT: L 255 MET cc_start: 0.8963 (mmp) cc_final: 0.8584 (mmm) REVERT: L 268 LYS cc_start: 0.6986 (pptt) cc_final: 0.6302 (mttp) REVERT: L 348 LEU cc_start: 0.8792 (tt) cc_final: 0.8508 (mt) REVERT: N 176 MET cc_start: 0.7419 (tmm) cc_final: 0.7191 (tmm) REVERT: N 316 GLN cc_start: 0.9511 (mp10) cc_final: 0.9164 (tt0) outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.2193 time to fit residues: 139.1421 Evaluate side-chains 272 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 181 optimal weight: 0.5980 chunk 230 optimal weight: 30.0000 chunk 242 optimal weight: 8.9990 chunk 177 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 302 optimal weight: 0.0270 chunk 312 optimal weight: 7.9990 chunk 416 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 212 GLN ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.079232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.061659 restraints weight = 255528.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.061299 restraints weight = 197961.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.061917 restraints weight = 152744.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.061946 restraints weight = 137903.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.062164 restraints weight = 122341.307| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36162 Z= 0.130 Angle : 0.596 13.302 48753 Z= 0.316 Chirality : 0.042 0.232 5352 Planarity : 0.003 0.083 6258 Dihedral : 4.988 28.554 4746 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.62 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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: -0.81 (0.12), residues: 4440 helix: 0.75 (0.13), residues: 1512 sheet: -0.39 (0.18), residues: 854 loop : -1.59 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 121 TYR 0.020 0.001 TYR E 83 PHE 0.014 0.001 PHE D 257 TRP 0.031 0.001 TRP J 338 HIS 0.004 0.001 HIS P 231 Details of bonding type rmsd covalent geometry : bond 0.00281 (36160) covalent geometry : angle 0.59550 (48749) SS BOND : bond 0.00283 ( 2) SS BOND : angle 1.34788 ( 4) hydrogen bonds : bond 0.03217 ( 1226) hydrogen bonds : angle 4.93059 ( 3471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 MET cc_start: 0.8305 (ppp) cc_final: 0.7990 (ppp) REVERT: P 255 MET cc_start: 0.8603 (mmm) cc_final: 0.7973 (mmm) REVERT: P 259 TYR cc_start: 0.5881 (m-80) cc_final: 0.5073 (m-80) REVERT: P 284 ARG cc_start: 0.8094 (ttt-90) cc_final: 0.7577 (ttp80) REVERT: P 288 MET cc_start: 0.8750 (mmp) cc_final: 0.8423 (mmp) REVERT: P 316 GLN cc_start: 0.9173 (mt0) cc_final: 0.8560 (mt0) REVERT: P 341 MET cc_start: 0.8003 (ppp) cc_final: 0.7768 (ppp) REVERT: B 24 TYR cc_start: 0.6911 (t80) cc_final: 0.6195 (t80) REVERT: D 117 MET cc_start: 0.8018 (pmm) cc_final: 0.7292 (pmm) REVERT: D 251 PHE cc_start: 0.9074 (t80) cc_final: 0.8709 (t80) REVERT: D 288 MET cc_start: 0.8468 (mtp) cc_final: 0.8222 (mtt) REVERT: A 290 GLU cc_start: 0.8725 (tt0) cc_final: 0.8030 (mt-10) REVERT: A 317 LEU cc_start: 0.9399 (tp) cc_final: 0.9164 (tp) REVERT: A 341 MET cc_start: 0.9226 (tmm) cc_final: 0.8751 (tmm) REVERT: C 117 MET cc_start: 0.8543 (pmm) cc_final: 0.7662 (pmm) REVERT: C 176 MET cc_start: 0.6754 (mpp) cc_final: 0.6309 (mpp) REVERT: C 228 MET cc_start: 0.2591 (pmm) cc_final: 0.1118 (mmm) REVERT: F 123 TYR cc_start: 0.8077 (m-80) cc_final: 0.7793 (m-80) REVERT: F 228 MET cc_start: 0.8471 (ptt) cc_final: 0.7961 (ptm) REVERT: F 269 MET cc_start: 0.7818 (ptm) cc_final: 0.6464 (ttp) REVERT: I 112 GLU cc_start: 0.8068 (mp0) cc_final: 0.7734 (mp0) REVERT: J 35 MET cc_start: 0.8953 (tpp) cc_final: 0.8696 (tpp) REVERT: J 178 MET cc_start: 0.8807 (mtp) cc_final: 0.8520 (mmt) REVERT: J 288 MET cc_start: 0.7828 (ppp) cc_final: 0.7595 (ppp) REVERT: G 41 PHE cc_start: 0.8483 (t80) cc_final: 0.8258 (t80) REVERT: G 48 MET cc_start: 0.7033 (mmt) cc_final: 0.6792 (mmt) REVERT: H 84 LEU cc_start: 0.8663 (mp) cc_final: 0.8372 (tp) REVERT: H 156 THR cc_start: 0.8993 (m) cc_final: 0.8701 (p) REVERT: H 254 MET cc_start: 0.8042 (ttm) cc_final: 0.7401 (ttm) REVERT: H 255 MET cc_start: 0.8999 (mmp) cc_final: 0.8488 (mmp) REVERT: H 288 MET cc_start: 0.8191 (mmp) cc_final: 0.7500 (ptp) REVERT: K 117 MET cc_start: 0.5083 (mpp) cc_final: 0.4857 (mpp) REVERT: K 142 LEU cc_start: 0.8685 (tt) cc_final: 0.8041 (mt) REVERT: K 288 MET cc_start: 0.8542 (mtt) cc_final: 0.8126 (ppp) REVERT: K 353 TYR cc_start: 0.8534 (t80) cc_final: 0.8303 (t80) REVERT: M 87 TYR cc_start: 0.8377 (m-10) cc_final: 0.8080 (m-10) REVERT: M 269 MET cc_start: 0.4205 (ttt) cc_final: 0.3888 (ttt) REVERT: M 280 TYR cc_start: 0.8744 (m-10) cc_final: 0.8526 (m-10) REVERT: M 312 HIS cc_start: 0.7791 (m170) cc_final: 0.7236 (m170) REVERT: M 316 GLN cc_start: 0.8859 (mt0) cc_final: 0.8389 (tt0) REVERT: M 345 HIS cc_start: 0.8730 (m90) cc_final: 0.8370 (m90) REVERT: L 228 MET cc_start: 0.4469 (ppp) cc_final: 0.3692 (ppp) REVERT: L 231 HIS cc_start: 0.8728 (p90) cc_final: 0.8488 (p90) REVERT: L 254 MET cc_start: 0.8899 (ppp) cc_final: 0.8398 (ppp) REVERT: L 255 MET cc_start: 0.8987 (mmp) cc_final: 0.8566 (mmm) REVERT: L 268 LYS cc_start: 0.7004 (pptt) cc_final: 0.6469 (mttp) REVERT: L 348 LEU cc_start: 0.8865 (tt) cc_final: 0.8640 (mt) REVERT: N 316 GLN cc_start: 0.9517 (mp10) cc_final: 0.9259 (tt0) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2097 time to fit residues: 119.6364 Evaluate side-chains 265 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 260 optimal weight: 0.0870 chunk 174 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 105 optimal weight: 0.0980 chunk 312 optimal weight: 4.9990 chunk 185 optimal weight: 0.2980 chunk 363 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN N 165 GLN N 312 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.080497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.062649 restraints weight = 255342.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.063119 restraints weight = 187945.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.063340 restraints weight = 140579.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.063603 restraints weight = 126501.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.063740 restraints weight = 111654.875| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36162 Z= 0.107 Angle : 0.584 12.452 48753 Z= 0.306 Chirality : 0.042 0.201 5352 Planarity : 0.003 0.084 6258 Dihedral : 4.740 28.882 4746 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 0.03 % Allowed : 0.72 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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: -0.63 (0.13), residues: 4440 helix: 0.91 (0.14), residues: 1518 sheet: -0.19 (0.18), residues: 848 loop : -1.55 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 185 TYR 0.020 0.001 TYR E 83 PHE 0.021 0.001 PHE B 199 TRP 0.022 0.001 TRP J 338 HIS 0.004 0.001 HIS K 345 Details of bonding type rmsd covalent geometry : bond 0.00224 (36160) covalent geometry : angle 0.58388 (48749) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.86655 ( 4) hydrogen bonds : bond 0.03036 ( 1226) hydrogen bonds : angle 4.70100 ( 3471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 MET cc_start: 0.8216 (ppp) cc_final: 0.7887 (ppp) REVERT: P 255 MET cc_start: 0.8562 (mmm) cc_final: 0.7958 (mmm) REVERT: P 259 TYR cc_start: 0.5802 (m-80) cc_final: 0.5061 (m-80) REVERT: P 284 ARG cc_start: 0.8150 (ttt-90) cc_final: 0.7668 (ttp80) REVERT: P 288 MET cc_start: 0.8540 (mmp) cc_final: 0.8257 (mmp) REVERT: P 316 GLN cc_start: 0.9053 (mt0) cc_final: 0.8260 (tt0) REVERT: B 24 TYR cc_start: 0.6254 (t80) cc_final: 0.5823 (t80) REVERT: D 48 MET cc_start: 0.6623 (mmt) cc_final: 0.6410 (mmt) REVERT: D 117 MET cc_start: 0.7551 (pmm) cc_final: 0.6847 (pmm) REVERT: A 35 MET cc_start: 0.7698 (ttm) cc_final: 0.7130 (ttm) REVERT: A 48 MET cc_start: 0.4974 (mtt) cc_final: 0.4720 (mtt) REVERT: A 198 ARG cc_start: 0.7058 (tpt90) cc_final: 0.6296 (mmm160) REVERT: A 341 MET cc_start: 0.8808 (tmm) cc_final: 0.8578 (tmm) REVERT: C 67 TRP cc_start: 0.7782 (m-10) cc_final: 0.7294 (m-10) REVERT: C 117 MET cc_start: 0.8391 (pmm) cc_final: 0.7401 (pmm) REVERT: C 176 MET cc_start: 0.6750 (mpp) cc_final: 0.5976 (mtm) REVERT: C 228 MET cc_start: 0.3246 (pmm) cc_final: 0.2137 (mmm) REVERT: F 48 MET cc_start: 0.6324 (tpt) cc_final: 0.5941 (tpp) REVERT: F 65 LEU cc_start: 0.8831 (mm) cc_final: 0.8523 (pt) REVERT: F 228 MET cc_start: 0.8143 (ptt) cc_final: 0.7518 (ptm) REVERT: F 269 MET cc_start: 0.7636 (ptm) cc_final: 0.6315 (ttp) REVERT: F 285 LEU cc_start: 0.9115 (tp) cc_final: 0.8866 (tp) REVERT: I 112 GLU cc_start: 0.7955 (mp0) cc_final: 0.7554 (mp0) REVERT: J 117 MET cc_start: 0.7834 (ptp) cc_final: 0.7524 (ptp) REVERT: J 178 MET cc_start: 0.8731 (mtp) cc_final: 0.8354 (mmt) REVERT: J 288 MET cc_start: 0.7819 (ppp) cc_final: 0.7596 (ppp) REVERT: G 48 MET cc_start: 0.7119 (mmt) cc_final: 0.6866 (mmt) REVERT: H 48 MET cc_start: 0.7952 (mmp) cc_final: 0.7749 (tpp) REVERT: H 84 LEU cc_start: 0.8350 (mp) cc_final: 0.8093 (tp) REVERT: H 156 THR cc_start: 0.8922 (m) cc_final: 0.8611 (p) REVERT: H 254 MET cc_start: 0.8101 (ttm) cc_final: 0.7455 (ttm) REVERT: H 255 MET cc_start: 0.9002 (mmp) cc_final: 0.8458 (mmp) REVERT: H 288 MET cc_start: 0.8079 (mmp) cc_final: 0.7426 (ptp) REVERT: K 117 MET cc_start: 0.5084 (mpp) cc_final: 0.4873 (mpp) REVERT: K 142 LEU cc_start: 0.8330 (tt) cc_final: 0.7936 (mt) REVERT: K 288 MET cc_start: 0.8476 (mtt) cc_final: 0.8094 (ppp) REVERT: M 176 MET cc_start: 0.5320 (mpp) cc_final: 0.4974 (mpp) REVERT: M 269 MET cc_start: 0.4142 (ttt) cc_final: 0.3690 (ttt) REVERT: M 280 TYR cc_start: 0.8581 (m-10) cc_final: 0.8379 (m-10) REVERT: M 288 MET cc_start: 0.9124 (ptp) cc_final: 0.8832 (ptp) REVERT: M 316 GLN cc_start: 0.8762 (mt0) cc_final: 0.8297 (tt0) REVERT: M 345 HIS cc_start: 0.8624 (m90) cc_final: 0.8302 (m90) REVERT: L 228 MET cc_start: 0.4294 (ppp) cc_final: 0.3593 (ppp) REVERT: L 231 HIS cc_start: 0.8669 (p90) cc_final: 0.8260 (p90) REVERT: L 254 MET cc_start: 0.8909 (ppp) cc_final: 0.8453 (ppp) REVERT: L 255 MET cc_start: 0.8949 (mmp) cc_final: 0.8535 (mmm) REVERT: L 268 LYS cc_start: 0.7126 (pptt) cc_final: 0.6694 (mttp) REVERT: L 348 LEU cc_start: 0.8868 (tt) cc_final: 0.8662 (mt) REVERT: N 316 GLN cc_start: 0.9455 (mp10) cc_final: 0.9240 (tt0) outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.2055 time to fit residues: 118.0839 Evaluate side-chains 257 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 365 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 263 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 228 optimal weight: 0.0770 chunk 172 optimal weight: 0.0970 chunk 287 optimal weight: 0.3980 chunk 189 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.080695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.062589 restraints weight = 253601.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.063630 restraints weight = 192247.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.063767 restraints weight = 130947.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.063985 restraints weight = 121158.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.064171 restraints weight = 104186.585| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36162 Z= 0.105 Angle : 0.582 11.463 48753 Z= 0.304 Chirality : 0.042 0.182 5352 Planarity : 0.003 0.081 6258 Dihedral : 4.593 26.096 4746 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.72 % Favored : 94.12 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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 (0.13), residues: 4440 helix: 0.96 (0.14), residues: 1521 sheet: -0.13 (0.18), residues: 850 loop : -1.51 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 139 TYR 0.017 0.001 TYR E 83 PHE 0.014 0.001 PHE C 257 TRP 0.050 0.001 TRP D 194 HIS 0.003 0.001 HIS L 231 Details of bonding type rmsd covalent geometry : bond 0.00221 (36160) covalent geometry : angle 0.58234 (48749) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.75572 ( 4) hydrogen bonds : bond 0.03019 ( 1226) hydrogen bonds : angle 4.60134 ( 3471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 MET cc_start: 0.8223 (ppp) cc_final: 0.7875 (ppp) REVERT: P 255 MET cc_start: 0.8536 (mmm) cc_final: 0.7923 (mmm) REVERT: P 259 TYR cc_start: 0.5593 (m-80) cc_final: 0.4957 (m-80) REVERT: P 284 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7687 (ttp80) REVERT: P 288 MET cc_start: 0.8481 (mmp) cc_final: 0.8166 (mmp) REVERT: P 316 GLN cc_start: 0.8979 (mt0) cc_final: 0.8423 (mt0) REVERT: P 341 MET cc_start: 0.7665 (ppp) cc_final: 0.7460 (ppp) REVERT: B 24 TYR cc_start: 0.6349 (t80) cc_final: 0.5941 (t80) REVERT: D 117 MET cc_start: 0.7511 (pmm) cc_final: 0.6778 (pmm) REVERT: A 198 ARG cc_start: 0.7104 (tpt90) cc_final: 0.6392 (mmm160) REVERT: A 341 MET cc_start: 0.8852 (tmm) cc_final: 0.8603 (tmm) REVERT: C 67 TRP cc_start: 0.7674 (m-10) cc_final: 0.7242 (m-10) REVERT: C 117 MET cc_start: 0.8450 (pmm) cc_final: 0.7465 (pmm) REVERT: C 176 MET cc_start: 0.6783 (mpp) cc_final: 0.5980 (mtm) REVERT: C 228 MET cc_start: 0.3071 (pmm) cc_final: 0.1899 (mmm) REVERT: F 269 MET cc_start: 0.7703 (ptm) cc_final: 0.6245 (ttp) REVERT: I 112 GLU cc_start: 0.7898 (mp0) cc_final: 0.7458 (mp0) REVERT: J 117 MET cc_start: 0.7961 (ptp) cc_final: 0.7698 (ptp) REVERT: J 176 MET cc_start: 0.2465 (mmt) cc_final: 0.1187 (mmt) REVERT: J 178 MET cc_start: 0.8775 (mtp) cc_final: 0.8419 (mmt) REVERT: J 288 MET cc_start: 0.7895 (ppp) cc_final: 0.7691 (ppp) REVERT: E 35 MET cc_start: 0.7637 (mmm) cc_final: 0.7122 (mmm) REVERT: G 41 PHE cc_start: 0.8252 (t80) cc_final: 0.8021 (t80) REVERT: G 48 MET cc_start: 0.7002 (mmt) cc_final: 0.6764 (mmt) REVERT: H 84 LEU cc_start: 0.8370 (mp) cc_final: 0.8095 (tp) REVERT: H 156 THR cc_start: 0.8851 (m) cc_final: 0.8554 (p) REVERT: H 254 MET cc_start: 0.8217 (ttm) cc_final: 0.7891 (ttm) REVERT: H 288 MET cc_start: 0.8022 (mmp) cc_final: 0.7381 (ptp) REVERT: K 117 MET cc_start: 0.5047 (mpp) cc_final: 0.4834 (mpp) REVERT: K 233 MET cc_start: -0.0191 (ppp) cc_final: -0.0561 (ppp) REVERT: K 288 MET cc_start: 0.8463 (mtt) cc_final: 0.8122 (ppp) REVERT: M 176 MET cc_start: 0.5193 (mpp) cc_final: 0.4781 (mpp) REVERT: M 269 MET cc_start: 0.3932 (ttt) cc_final: 0.3474 (ttt) REVERT: M 316 GLN cc_start: 0.8753 (mt0) cc_final: 0.8323 (tt0) REVERT: M 345 HIS cc_start: 0.8659 (m90) cc_final: 0.8322 (m90) REVERT: L 228 MET cc_start: 0.4328 (ppp) cc_final: 0.3570 (ppp) REVERT: L 231 HIS cc_start: 0.8508 (p90) cc_final: 0.8277 (p90) REVERT: L 254 MET cc_start: 0.8901 (ppp) cc_final: 0.8337 (ppp) REVERT: L 255 MET cc_start: 0.8958 (mmp) cc_final: 0.8481 (mmt) REVERT: L 268 LYS cc_start: 0.7242 (pptt) cc_final: 0.6884 (mttp) REVERT: N 312 HIS cc_start: 0.8199 (m90) cc_final: 0.7991 (m90) REVERT: N 316 GLN cc_start: 0.9418 (mp10) cc_final: 0.9197 (tt0) REVERT: N 349 VAL cc_start: 0.8141 (t) cc_final: 0.7576 (p) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.1913 time to fit residues: 111.4637 Evaluate side-chains 262 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 25 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 190 optimal weight: 0.6980 chunk 387 optimal weight: 7.9990 chunk 365 optimal weight: 3.9990 chunk 217 optimal weight: 0.0050 chunk 42 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 370 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 ASN J 320 GLN ** H 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.077777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.059653 restraints weight = 255067.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.059986 restraints weight = 166015.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.060311 restraints weight = 127026.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.060370 restraints weight = 114359.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.060579 restraints weight = 104389.792| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36162 Z= 0.183 Angle : 0.644 12.615 48753 Z= 0.341 Chirality : 0.043 0.194 5352 Planarity : 0.004 0.073 6258 Dihedral : 4.996 26.628 4746 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.69 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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: -0.74 (0.12), residues: 4440 helix: 0.77 (0.13), residues: 1520 sheet: -0.32 (0.18), residues: 897 loop : -1.56 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 221 TYR 0.021 0.002 TYR J 87 PHE 0.027 0.002 PHE C 32 TRP 0.034 0.002 TRP D 194 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00393 (36160) covalent geometry : angle 0.64447 (48749) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.72027 ( 4) hydrogen bonds : bond 0.03352 ( 1226) hydrogen bonds : angle 4.95911 ( 3471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 254 MET cc_start: 0.8298 (ppp) cc_final: 0.7920 (ppp) REVERT: P 255 MET cc_start: 0.8627 (mmm) cc_final: 0.8388 (mmm) REVERT: P 284 ARG cc_start: 0.8094 (ttt-90) cc_final: 0.7616 (ttp80) REVERT: P 288 MET cc_start: 0.8734 (mmp) cc_final: 0.8418 (mmp) REVERT: P 316 GLN cc_start: 0.9213 (mt0) cc_final: 0.8624 (mt0) REVERT: B 24 TYR cc_start: 0.7086 (t80) cc_final: 0.6564 (t80) REVERT: D 34 TYR cc_start: 0.7739 (t80) cc_final: 0.7288 (t80) REVERT: D 117 MET cc_start: 0.7869 (pmm) cc_final: 0.7124 (pmm) REVERT: A 269 MET cc_start: 0.8495 (mpp) cc_final: 0.8125 (mmm) REVERT: A 290 GLU cc_start: 0.8672 (tt0) cc_final: 0.8009 (mt-10) REVERT: A 341 MET cc_start: 0.9223 (tmm) cc_final: 0.8746 (tmm) REVERT: C 48 MET cc_start: 0.5878 (mmt) cc_final: 0.4663 (tpp) REVERT: C 117 MET cc_start: 0.8633 (pmm) cc_final: 0.7816 (pmm) REVERT: C 176 MET cc_start: 0.6954 (mpp) cc_final: 0.6247 (mtm) REVERT: C 228 MET cc_start: 0.2996 (pmm) cc_final: 0.1767 (mmm) REVERT: F 228 MET cc_start: 0.8419 (ptt) cc_final: 0.7830 (ptm) REVERT: F 269 MET cc_start: 0.7982 (ptm) cc_final: 0.6294 (ttp) REVERT: F 290 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8935 (mp0) REVERT: I 35 MET cc_start: 0.8562 (tpt) cc_final: 0.8253 (mmm) REVERT: I 112 GLU cc_start: 0.8020 (mp0) cc_final: 0.7642 (mp0) REVERT: J 35 MET cc_start: 0.8683 (tpp) cc_final: 0.8402 (tpp) REVERT: J 176 MET cc_start: 0.2636 (mmt) cc_final: 0.2111 (mmt) REVERT: J 178 MET cc_start: 0.8869 (mtp) cc_final: 0.8588 (mmt) REVERT: G 41 PHE cc_start: 0.8673 (t80) cc_final: 0.8381 (t80) REVERT: H 84 LEU cc_start: 0.8531 (mp) cc_final: 0.8298 (tp) REVERT: H 156 THR cc_start: 0.8966 (m) cc_final: 0.8699 (p) REVERT: H 254 MET cc_start: 0.8164 (ttm) cc_final: 0.7879 (ttm) REVERT: K 142 LEU cc_start: 0.8654 (pp) cc_final: 0.8386 (pp) REVERT: K 176 MET cc_start: 0.6453 (mmp) cc_final: 0.6237 (mtm) REVERT: K 288 MET cc_start: 0.8490 (mtt) cc_final: 0.8137 (ppp) REVERT: K 351 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8065 (tm-30) REVERT: M 176 MET cc_start: 0.6045 (mpp) cc_final: 0.5643 (mpp) REVERT: M 269 MET cc_start: 0.4193 (ttt) cc_final: 0.2955 (ttt) REVERT: M 316 GLN cc_start: 0.8732 (mt0) cc_final: 0.8214 (tt0) REVERT: M 345 HIS cc_start: 0.8704 (m90) cc_final: 0.8363 (m90) REVERT: L 228 MET cc_start: 0.4642 (ppp) cc_final: 0.3835 (ppp) REVERT: L 231 HIS cc_start: 0.8668 (p90) cc_final: 0.8418 (p90) REVERT: L 254 MET cc_start: 0.8888 (ppp) cc_final: 0.8388 (ppp) REVERT: L 255 MET cc_start: 0.8947 (mmp) cc_final: 0.8536 (mmt) REVERT: L 268 LYS cc_start: 0.7319 (pptt) cc_final: 0.6989 (mttp) REVERT: N 284 ARG cc_start: 0.7224 (ttt-90) cc_final: 0.6932 (mtp180) REVERT: N 316 GLN cc_start: 0.9517 (mp10) cc_final: 0.9208 (tt0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2229 time to fit residues: 119.2388 Evaluate side-chains 250 residues out of total 3907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 153 optimal weight: 3.9990 chunk 302 optimal weight: 0.0270 chunk 200 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 136 optimal weight: 0.0030 chunk 141 optimal weight: 20.0000 chunk 262 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 chunk 416 optimal weight: 0.5980 chunk 217 optimal weight: 0.1980 overall best weight: 0.2848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN L 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.080272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.062066 restraints weight = 253799.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.062674 restraints weight = 200799.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.063221 restraints weight = 141239.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.063428 restraints weight = 114458.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.063539 restraints weight = 104258.727| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36162 Z= 0.104 Angle : 0.589 12.518 48753 Z= 0.305 Chirality : 0.042 0.180 5352 Planarity : 0.003 0.083 6258 Dihedral : 4.616 23.902 4746 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.01 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.30 % 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 (0.13), residues: 4440 helix: 0.91 (0.14), residues: 1523 sheet: -0.11 (0.18), residues: 877 loop : -1.49 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 221 TYR 0.019 0.001 TYR E 83 PHE 0.012 0.001 PHE C 257 TRP 0.035 0.001 TRP D 194 HIS 0.004 0.001 HIS K 345 Details of bonding type rmsd covalent geometry : bond 0.00217 (36160) covalent geometry : angle 0.58847 (48749) SS BOND : bond 0.00306 ( 2) SS BOND : angle 0.92460 ( 4) hydrogen bonds : bond 0.02990 ( 1226) hydrogen bonds : angle 4.64596 ( 3471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6376.55 seconds wall clock time: 111 minutes 42.36 seconds (6702.36 seconds total)