Starting phenix.real_space_refine on Fri Feb 6 20:42:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1h_70007/02_2026/9o1h_70007_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1h_70007/02_2026/9o1h_70007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1h_70007/02_2026/9o1h_70007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1h_70007/02_2026/9o1h_70007.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1h_70007/02_2026/9o1h_70007_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1h_70007/02_2026/9o1h_70007_neut.cif" } resolution = 2.17 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= 0.003 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 93 5.16 5 C 17327 2.51 5 N 4788 2.21 5 O 5408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27636 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3823 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain: "B" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3808 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain: "C" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3823 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain: "D" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 435} Chain: "F" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3464 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 20, 'TRANS': 435} Chain: "G" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2074 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 261} Chain breaks: 2 Chain: "H" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 929 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Chain: "W" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1345 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain: "X" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 655 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "Y" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 608 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.19 Number of scatterers: 27636 At special positions: 0 Unit cell: (126.99, 136.12, 178.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 93 16.00 P 15 15.00 Mg 5 11.99 O 5408 8.00 N 4788 7.00 C 17327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 23 sheets defined 52.8% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.887A pdb=" N ARG A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 3.505A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.601A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 378 through 383 removed outlier: 3.562A pdb=" N ALA A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 404 removed outlier: 4.409A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.817A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.518A pdb=" N MET A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.606A pdb=" N SER A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.587A pdb=" N ARG B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 4.568A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.743A pdb=" N HIS B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.620A pdb=" N SER B 348 " --> pdb=" O THR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.531A pdb=" N ALA B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.595A pdb=" N GLU B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.502A pdb=" N ALA B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.670A pdb=" N ARG C 140 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix removed outlier: 4.346A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.700A pdb=" N HIS C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 391 through 405 removed outlier: 4.112A pdb=" N ARG C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 415 through 433 removed outlier: 3.577A pdb=" N LYS C 433 " --> pdb=" O THR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 461 through 480 removed outlier: 4.446A pdb=" N GLY C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 512 removed outlier: 3.612A pdb=" N ALA C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.705A pdb=" N GLN D 124 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 172 Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 217 through 238 removed outlier: 5.313A pdb=" N ALA D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.794A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.662A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.508A pdb=" N PHE D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 355 through 382 removed outlier: 4.851A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 405 Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 424 through 438 Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'D' and resid 453 through 463 removed outlier: 3.791A pdb=" N ALA D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.569A pdb=" N GLN E 124 " --> pdb=" O TYR E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 172 Processing helix chain 'E' and resid 187 through 201 removed outlier: 3.544A pdb=" N GLY E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 217 through 238 removed outlier: 3.503A pdb=" N ARG E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 261 removed outlier: 3.861A pdb=" N THR E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 275 through 287 removed outlier: 4.250A pdb=" N ARG E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 327 through 333 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 375 Processing helix chain 'E' and resid 375 through 383 Processing helix chain 'E' and resid 384 through 387 Processing helix chain 'E' and resid 388 through 405 Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 424 through 438 Processing helix chain 'E' and resid 444 through 448 Processing helix chain 'E' and resid 453 through 461 removed outlier: 3.675A pdb=" N ALA E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.739A pdb=" N GLN F 124 " --> pdb=" O TYR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 142 Processing helix chain 'F' and resid 159 through 176 removed outlier: 3.559A pdb=" N ALA F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 201 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 217 through 239 removed outlier: 3.589A pdb=" N ARG F 221 " --> pdb=" O PRO F 217 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ALA F 225 " --> pdb=" O ARG F 221 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE F 235 " --> pdb=" O MET F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.738A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 275 through 285 removed outlier: 3.596A pdb=" N LEU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.518A pdb=" N ALA F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 334 Processing helix chain 'F' and resid 350 through 382 removed outlier: 8.107A pdb=" N GLN F 356 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N ASP F 357 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS F 358 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 removed outlier: 3.514A pdb=" N LEU F 387 " --> pdb=" O MET F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 438 Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 453 through 463 removed outlier: 3.739A pdb=" N ALA F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 41 removed outlier: 3.952A pdb=" N ILE G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 60 removed outlier: 3.517A pdb=" N ALA G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 49 " --> pdb=" O TYR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 90 through 110 removed outlier: 3.734A pdb=" N LEU G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 removed outlier: 3.585A pdb=" N ALA G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 162 removed outlier: 4.040A pdb=" N LEU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 284 removed outlier: 3.689A pdb=" N VAL G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 103 removed outlier: 3.642A pdb=" N ALA H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 130 removed outlier: 3.581A pdb=" N ALA H 119 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 22 Proline residue: W 10 - end of helix Processing helix chain 'W' and resid 24 through 41 removed outlier: 3.762A pdb=" N SER W 29 " --> pdb=" O LEU W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 49 Processing helix chain 'W' and resid 54 through 67 Processing helix chain 'W' and resid 68 through 70 No H-bonds generated for 'chain 'W' and resid 68 through 70' Processing helix chain 'W' and resid 71 through 84 Processing helix chain 'W' and resid 86 through 88 No H-bonds generated for 'chain 'W' and resid 86 through 88' Processing helix chain 'W' and resid 89 through 106 Processing helix chain 'W' and resid 119 through 135 removed outlier: 3.537A pdb=" N LYS W 125 " --> pdb=" O GLU W 121 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS W 128 " --> pdb=" O ASP W 124 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA W 129 " --> pdb=" O LYS W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 178 removed outlier: 3.639A pdb=" N LEU W 176 " --> pdb=" O LEU W 172 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS W 177 " --> pdb=" O ALA W 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 133 removed outlier: 3.531A pdb=" N ASN X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP X 118 " --> pdb=" O ASN X 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA X 119 " --> pdb=" O SER X 115 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG X 121 " --> pdb=" O LYS X 117 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA X 122 " --> pdb=" O ASP X 118 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA X 126 " --> pdb=" O ALA X 122 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY X 131 " --> pdb=" O LEU X 127 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA X 132 " --> pdb=" O ALA X 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 155 removed outlier: 4.668A pdb=" N ALA X 142 " --> pdb=" O ALA X 138 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN X 143 " --> pdb=" O SER X 139 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS X 145 " --> pdb=" O ASP X 141 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 155 removed outlier: 3.576A pdb=" N LYS Y 134 " --> pdb=" O THR Y 130 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER Y 139 " --> pdb=" O ILE Y 135 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA Y 142 " --> pdb=" O ALA Y 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU Y 146 " --> pdb=" O ALA Y 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 36 removed outlier: 6.683A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 39 through 44 current: chain 'A' and resid 60 through 67 removed outlier: 5.863A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 72 through 76 current: chain 'F' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 23 current: chain 'F' and resid 44 through 52 removed outlier: 5.754A pdb=" N VAL F 47 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 59 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 60 current: chain 'W' and resid 137 through 140 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 137 through 140 current: chain 'W' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.117A pdb=" N ALA A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.502A pdb=" N VAL A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 261 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.593A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.720A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 110 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 108 through 110 current: chain 'B' and resid 222 through 227 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 222 through 227 current: chain 'B' and resid 323 through 332 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 323 through 332 current: chain 'B' and resid 375 through 376 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 67 removed outlier: 4.428A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET C 53 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG E 57 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN E 50 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL E 55 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.984A pdb=" N ALA C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 109 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 108 through 109 current: chain 'C' and resid 222 through 228 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 222 through 228 current: chain 'C' and resid 323 through 332 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 323 through 332 current: chain 'C' and resid 375 through 376 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.541A pdb=" N VAL C 160 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 9 through 16 removed outlier: 5.928A pdb=" N ILE D 12 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU D 23 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 14 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL D 55 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN D 50 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 57 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 81 through 83 Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.204A pdb=" N MET D 93 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER D 179 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL D 210 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE D 181 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY D 212 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY D 183 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 178 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N TYR D 302 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS D 149 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL D 324 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY D 151 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.111A pdb=" N PHE D 144 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 81 through 83 Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.624A pdb=" N MET E 93 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR E 178 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 150 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL E 301 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU E 152 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS E 149 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL E 324 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY E 151 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.481A pdb=" N PHE E 144 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AC2, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.303A pdb=" N MET F 93 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLN F 213 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR F 178 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL F 150 " --> pdb=" O GLN F 299 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS F 149 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL F 324 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY F 151 " --> pdb=" O VAL F 324 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 135 through 137 removed outlier: 6.301A pdb=" N VAL G 117 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE G 79 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ASN G 173 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N PHE G 175 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 206 through 208 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 206 through 208 current: chain 'H' and resid 15 through 17 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 15 through 17 current: chain 'H' and resid 68 through 72 Processing sheet with id=AC5, first strand: chain 'H' and resid 33 through 35 1381 hydrogen bonds defined for protein. 3942 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: 4.70 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5214 1.31 - 1.43: 6226 1.43 - 1.56: 16401 1.56 - 1.69: 13 1.69 - 1.82: 169 Bond restraints: 28023 Sorted by residual: bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.350 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" CZ ARG B 284 " pdb=" NH1 ARG B 284 " ideal model delta sigma weight residual 1.323 1.248 0.075 1.40e-02 5.10e+03 2.84e+01 bond pdb=" C5 ADP E 501 " pdb=" C6 ADP E 501 " ideal model delta sigma weight residual 1.490 1.390 0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 28018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 36917 4.25 - 8.50: 961 8.50 - 12.75: 19 12.75 - 16.99: 5 16.99 - 21.24: 4 Bond angle restraints: 37906 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.92 17.95 1.00e+00 1.00e+00 3.22e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.47 17.40 1.00e+00 1.00e+00 3.03e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 123.96 15.91 1.00e+00 1.00e+00 2.53e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 122.98 13.85 1.00e+00 1.00e+00 1.92e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 123.22 13.61 1.00e+00 1.00e+00 1.85e+02 ... (remaining 37901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 16806 34.26 - 68.52: 267 68.52 - 102.78: 20 102.78 - 137.04: 3 137.04 - 171.31: 3 Dihedral angle restraints: 17099 sinusoidal: 6797 harmonic: 10302 Sorted by residual: dihedral pdb=" C2' ADP E 501 " pdb=" C1' ADP E 501 " pdb=" N9 ADP E 501 " pdb=" C4 ADP E 501 " ideal model delta sinusoidal sigma weight residual 91.55 -79.76 171.31 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.40 -160.40 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 96.16 -156.16 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 17096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 3200 0.112 - 0.223: 1036 0.223 - 0.335: 88 0.335 - 0.446: 18 0.446 - 0.558: 6 Chirality restraints: 4348 Sorted by residual: chirality pdb=" CA ASP X 88 " pdb=" N ASP X 88 " pdb=" C ASP X 88 " pdb=" CB ASP X 88 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CA GLN X 123 " pdb=" N GLN X 123 " pdb=" C GLN X 123 " pdb=" CB GLN X 123 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CA LYS G 121 " pdb=" N LYS G 121 " pdb=" C LYS G 121 " pdb=" CB LYS G 121 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 4345 not shown) Planarity restraints: 4946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP E 501 " -0.490 2.00e-02 2.50e+03 1.99e-01 1.08e+03 pdb=" C2 ADP E 501 " 0.096 2.00e-02 2.50e+03 pdb=" C4 ADP E 501 " 0.103 2.00e-02 2.50e+03 pdb=" C5 ADP E 501 " 0.028 2.00e-02 2.50e+03 pdb=" C6 ADP E 501 " -0.092 2.00e-02 2.50e+03 pdb=" C8 ADP E 501 " 0.228 2.00e-02 2.50e+03 pdb=" N1 ADP E 501 " -0.052 2.00e-02 2.50e+03 pdb=" N3 ADP E 501 " 0.153 2.00e-02 2.50e+03 pdb=" N6 ADP E 501 " -0.229 2.00e-02 2.50e+03 pdb=" N7 ADP E 501 " 0.101 2.00e-02 2.50e+03 pdb=" N9 ADP E 501 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 475 " 0.184 2.00e-02 2.50e+03 1.04e-01 2.14e+02 pdb=" CG TYR C 475 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR C 475 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TYR C 475 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 TYR C 475 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR C 475 " -0.069 2.00e-02 2.50e+03 pdb=" CZ TYR C 475 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR C 475 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 121 " -0.131 2.00e-02 2.50e+03 7.26e-02 1.05e+02 pdb=" CG TYR F 121 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 121 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR F 121 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR F 121 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR F 121 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR F 121 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 121 " -0.115 2.00e-02 2.50e+03 ... (remaining 4943 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 10 2.39 - 3.02: 14148 3.02 - 3.64: 39550 3.64 - 4.27: 63597 4.27 - 4.90: 105349 Nonbonded interactions: 222654 Sorted by model distance: nonbonded pdb=" OG1 THR C 177 " pdb="MG MG C 601 " model vdw 1.759 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.844 2.170 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.884 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.892 2.170 nonbonded pdb=" OE1 GLU E 186 " pdb="MG MG E 502 " model vdw 1.907 2.170 ... (remaining 222649 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 9 through 601) selection = chain 'B' selection = (chain 'C' and resid 9 through 601) } ncs_group { reference = (chain 'D' and resid 8 through 501) selection = (chain 'E' and resid 8 through 501) selection = chain 'F' } ncs_group { reference = (chain 'X' and resid 75 through 155) selection = chain 'Y' } 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 individual isotropic 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: 4.010 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.320 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.013 0.143 28023 Z= 0.812 Angle : 1.855 21.243 37906 Z= 1.278 Chirality : 0.102 0.558 4348 Planarity : 0.016 0.377 4946 Dihedral : 12.595 171.306 10527 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 0.28 % Allowed : 3.41 % Favored : 96.31 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 3598 helix: -0.70 (0.11), residues: 1603 sheet: -0.03 (0.21), residues: 473 loop : -0.75 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.002 ARG C 251 TYR 0.184 0.016 TYR C 475 PHE 0.080 0.012 PHE G 67 TRP 0.087 0.019 TRP G 203 HIS 0.015 0.003 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.01269 (28023) covalent geometry : angle 1.85498 (37906) hydrogen bonds : bond 0.22018 ( 1381) hydrogen bonds : angle 7.45969 ( 3942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 344 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 MET cc_start: 0.8486 (mtm) cc_final: 0.8134 (mtm) REVERT: C 422 LEU cc_start: 0.7650 (tt) cc_final: 0.7225 (tm) REVERT: E 61 MET cc_start: 0.8416 (mmt) cc_final: 0.8164 (mmp) REVERT: F 280 MET cc_start: 0.8824 (tpp) cc_final: 0.8351 (tpp) outliers start: 8 outliers final: 2 residues processed: 350 average time/residue: 0.8622 time to fit residues: 338.8783 Evaluate side-chains 177 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain X residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 470 GLN C 295 HIS D 248 ASN D 437 ASN F 437 ASN G 60 ASN G 94 ASN H 60 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.120917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084696 restraints weight = 45486.495| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.66 r_work: 0.3217 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28023 Z= 0.143 Angle : 0.584 7.008 37906 Z= 0.316 Chirality : 0.044 0.232 4348 Planarity : 0.004 0.043 4946 Dihedral : 8.475 166.307 4061 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.14 % Favored : 98.83 % Rotamer: Outliers : 0.98 % Allowed : 8.12 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3598 helix: 1.49 (0.13), residues: 1627 sheet: 0.30 (0.21), residues: 500 loop : -0.28 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 189 TYR 0.016 0.001 TYR D 252 PHE 0.014 0.001 PHE E 194 TRP 0.011 0.001 TRP W 28 HIS 0.006 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00271 (28023) covalent geometry : angle 0.58368 (37906) hydrogen bonds : bond 0.06537 ( 1381) hydrogen bonds : angle 5.02954 ( 3942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6991 (mp-120) REVERT: A 419 ARG cc_start: 0.7504 (ttm110) cc_final: 0.7128 (ttp-110) REVERT: B 11 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7023 (tp30) REVERT: B 95 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8132 (pp) REVERT: B 211 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7797 (ttp-110) REVERT: C 49 MET cc_start: 0.9158 (mtm) cc_final: 0.8857 (mtm) REVERT: C 231 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: C 507 LYS cc_start: 0.7852 (tmtt) cc_final: 0.7559 (tmtt) REVERT: D 381 ILE cc_start: 0.7942 (mm) cc_final: 0.7732 (tp) REVERT: D 450 MET cc_start: 0.8597 (mmt) cc_final: 0.8077 (mmm) REVERT: E 61 MET cc_start: 0.9220 (mmt) cc_final: 0.9002 (mmp) REVERT: G 68 MET cc_start: 0.5840 (mtm) cc_final: 0.5612 (mtm) REVERT: G 186 GLU cc_start: 0.5638 (pt0) cc_final: 0.5420 (mt-10) REVERT: H 76 MET cc_start: 0.3860 (ttm) cc_final: 0.3367 (mmp) REVERT: H 77 VAL cc_start: 0.4669 (OUTLIER) cc_final: 0.4259 (p) REVERT: W 158 ASP cc_start: 0.7734 (m-30) cc_final: 0.7519 (m-30) outliers start: 28 outliers final: 4 residues processed: 213 average time/residue: 0.8476 time to fit residues: 204.7326 Evaluate side-chains 169 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 338 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 334 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 305 optimal weight: 20.0000 chunk 80 optimal weight: 0.2980 chunk 223 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 HIS B 470 GLN D 248 ASN E 14 GLN F 358 HIS H 39 HIS Y 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.116182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079414 restraints weight = 44891.447| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.77 r_work: 0.3092 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 28023 Z= 0.213 Angle : 0.656 11.709 37906 Z= 0.349 Chirality : 0.047 0.184 4348 Planarity : 0.005 0.073 4946 Dihedral : 8.878 174.768 4058 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 1.36 % Allowed : 8.43 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.14), residues: 3598 helix: 1.73 (0.13), residues: 1619 sheet: 0.28 (0.20), residues: 539 loop : -0.15 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 251 TYR 0.019 0.002 TYR D 252 PHE 0.016 0.002 PHE C 250 TRP 0.009 0.002 TRP C 139 HIS 0.007 0.002 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00498 (28023) covalent geometry : angle 0.65628 (37906) hydrogen bonds : bond 0.07139 ( 1381) hydrogen bonds : angle 4.93319 ( 3942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6993 (mp-120) REVERT: A 419 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7200 (ttp-110) REVERT: B 11 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7078 (tp30) REVERT: B 123 ASP cc_start: 0.7603 (m-30) cc_final: 0.7300 (m-30) REVERT: C 231 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: C 507 LYS cc_start: 0.7745 (tmtt) cc_final: 0.7527 (tmtt) REVERT: D 450 MET cc_start: 0.8764 (mmt) cc_final: 0.8303 (mmm) REVERT: E 61 MET cc_start: 0.9264 (mmt) cc_final: 0.8969 (mmp) REVERT: E 129 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: E 248 ASN cc_start: 0.8079 (t0) cc_final: 0.7847 (t0) REVERT: G 68 MET cc_start: 0.5877 (mtm) cc_final: 0.5667 (mtm) REVERT: H 76 MET cc_start: 0.3990 (ttm) cc_final: 0.3624 (mmm) REVERT: H 77 VAL cc_start: 0.4567 (OUTLIER) cc_final: 0.4256 (p) REVERT: W 158 ASP cc_start: 0.7756 (m-30) cc_final: 0.7517 (m-30) outliers start: 39 outliers final: 10 residues processed: 211 average time/residue: 0.8371 time to fit residues: 200.5253 Evaluate side-chains 174 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 70 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN E 175 HIS F 356 GLN H 39 HIS Y 147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.115360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078075 restraints weight = 44882.881| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.63 r_work: 0.3094 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28023 Z= 0.202 Angle : 0.632 10.620 37906 Z= 0.335 Chirality : 0.047 0.187 4348 Planarity : 0.005 0.070 4946 Dihedral : 8.828 177.651 4058 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.28 % Rotamer: Outliers : 1.53 % Allowed : 9.02 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.14), residues: 3598 helix: 1.77 (0.13), residues: 1628 sheet: 0.21 (0.21), residues: 555 loop : -0.06 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 251 TYR 0.018 0.002 TYR D 252 PHE 0.016 0.002 PHE C 456 TRP 0.007 0.001 TRP A 139 HIS 0.006 0.002 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00468 (28023) covalent geometry : angle 0.63216 (37906) hydrogen bonds : bond 0.06769 ( 1381) hydrogen bonds : angle 4.82415 ( 3942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7005 (mp-120) REVERT: B 95 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8370 (pp) REVERT: C 16 ARG cc_start: 0.7336 (ptt90) cc_final: 0.7100 (ptt90) REVERT: C 231 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: C 407 PHE cc_start: 0.4435 (OUTLIER) cc_final: 0.4142 (m-10) REVERT: C 507 LYS cc_start: 0.7659 (tmtt) cc_final: 0.7427 (tmtt) REVERT: D 450 MET cc_start: 0.8798 (mmt) cc_final: 0.8336 (mmm) REVERT: E 61 MET cc_start: 0.9290 (mmt) cc_final: 0.8996 (mmp) REVERT: E 129 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: E 130 LEU cc_start: 0.9012 (tp) cc_final: 0.8727 (tm) REVERT: F 142 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.8000 (p) REVERT: G 68 MET cc_start: 0.6005 (mtm) cc_final: 0.5733 (mtm) REVERT: H 76 MET cc_start: 0.4055 (ttm) cc_final: 0.3699 (mmm) REVERT: H 77 VAL cc_start: 0.4381 (OUTLIER) cc_final: 0.4137 (p) REVERT: W 158 ASP cc_start: 0.7587 (m-30) cc_final: 0.7301 (m-30) outliers start: 44 outliers final: 15 residues processed: 195 average time/residue: 0.7819 time to fit residues: 174.7331 Evaluate side-chains 175 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain W residue 148 LEU Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 345 optimal weight: 5.9990 chunk 291 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 236 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 335 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 470 GLN D 248 ASN G 92 ASN H 39 HIS Y 147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.116872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079935 restraints weight = 44828.810| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.61 r_work: 0.3126 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28023 Z= 0.132 Angle : 0.532 7.141 37906 Z= 0.282 Chirality : 0.043 0.180 4348 Planarity : 0.004 0.052 4946 Dihedral : 8.366 164.764 4058 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.42 % Rotamer: Outliers : 1.11 % Allowed : 9.51 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.14), residues: 3598 helix: 2.10 (0.13), residues: 1614 sheet: 0.29 (0.20), residues: 571 loop : 0.02 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 419 TYR 0.018 0.001 TYR D 252 PHE 0.033 0.001 PHE C 456 TRP 0.005 0.001 TRP A 139 HIS 0.005 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00278 (28023) covalent geometry : angle 0.53228 (37906) hydrogen bonds : bond 0.05673 ( 1381) hydrogen bonds : angle 4.61532 ( 3942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6630 (mp-120) REVERT: C 231 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: C 407 PHE cc_start: 0.4578 (OUTLIER) cc_final: 0.4237 (m-10) REVERT: C 422 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6595 (tm) REVERT: C 426 GLN cc_start: 0.7291 (mt0) cc_final: 0.6757 (mt0) REVERT: C 440 MET cc_start: 0.8846 (mtp) cc_final: 0.8616 (ttm) REVERT: D 384 MET cc_start: 0.8154 (ttt) cc_final: 0.7823 (mtp) REVERT: D 450 MET cc_start: 0.8739 (mmt) cc_final: 0.8382 (mmm) REVERT: E 61 MET cc_start: 0.9282 (mmt) cc_final: 0.8999 (mmp) REVERT: E 129 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: E 130 LEU cc_start: 0.8951 (tp) cc_final: 0.8681 (tm) REVERT: F 371 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7473 (mmm-85) REVERT: G 37 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6712 (mmp) REVERT: G 39 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6552 (mtm) REVERT: G 68 MET cc_start: 0.5971 (mtm) cc_final: 0.5748 (mtm) REVERT: G 178 THR cc_start: 0.8002 (m) cc_final: 0.7540 (t) REVERT: H 76 MET cc_start: 0.4222 (ttm) cc_final: 0.3879 (mmm) REVERT: H 77 VAL cc_start: 0.4271 (OUTLIER) cc_final: 0.4043 (p) REVERT: W 133 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.5859 (ttt-90) REVERT: W 158 ASP cc_start: 0.7593 (m-30) cc_final: 0.7335 (m-30) outliers start: 32 outliers final: 10 residues processed: 179 average time/residue: 0.8235 time to fit residues: 168.3366 Evaluate side-chains 170 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain W residue 133 ARG Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 277 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 310 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS B 470 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 HIS Y 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.115152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078113 restraints weight = 44655.226| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.59 r_work: 0.3090 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28023 Z= 0.209 Angle : 0.629 11.533 37906 Z= 0.331 Chirality : 0.047 0.183 4348 Planarity : 0.005 0.074 4946 Dihedral : 8.597 159.558 4058 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.64 % Allowed : 9.40 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.14), residues: 3598 helix: 1.90 (0.13), residues: 1625 sheet: 0.24 (0.20), residues: 565 loop : -0.04 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 169 TYR 0.019 0.002 TYR D 252 PHE 0.024 0.002 PHE C 456 TRP 0.006 0.001 TRP E 112 HIS 0.005 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00493 (28023) covalent geometry : angle 0.62923 (37906) hydrogen bonds : bond 0.06641 ( 1381) hydrogen bonds : angle 4.75516 ( 3942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 366 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6209 (mmp-170) REVERT: A 409 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6618 (mp-120) REVERT: B 95 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8402 (pp) REVERT: C 231 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: C 407 PHE cc_start: 0.4632 (OUTLIER) cc_final: 0.4300 (m-10) REVERT: C 426 GLN cc_start: 0.7349 (mt0) cc_final: 0.6920 (mt0) REVERT: C 464 LYS cc_start: 0.8488 (mttt) cc_final: 0.7620 (tmtt) REVERT: D 65 GLU cc_start: 0.6123 (pm20) cc_final: 0.5902 (pm20) REVERT: D 128 ASN cc_start: 0.8189 (m-40) cc_final: 0.7841 (p0) REVERT: D 384 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7849 (mtp) REVERT: D 450 MET cc_start: 0.8799 (mmt) cc_final: 0.8322 (mmm) REVERT: E 61 MET cc_start: 0.9288 (mmt) cc_final: 0.8995 (mmp) REVERT: E 109 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: E 129 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: E 130 LEU cc_start: 0.8994 (tp) cc_final: 0.8716 (tm) REVERT: G 37 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6710 (mmp) REVERT: G 68 MET cc_start: 0.6004 (mtm) cc_final: 0.5751 (mtm) REVERT: G 178 THR cc_start: 0.8010 (m) cc_final: 0.7556 (t) REVERT: H 76 MET cc_start: 0.4159 (ttm) cc_final: 0.3802 (mmm) REVERT: H 77 VAL cc_start: 0.4171 (OUTLIER) cc_final: 0.3965 (p) REVERT: W 133 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.5831 (ttt-90) REVERT: W 158 ASP cc_start: 0.7597 (m-30) cc_final: 0.7309 (m-30) outliers start: 47 outliers final: 16 residues processed: 191 average time/residue: 0.7875 time to fit residues: 171.8933 Evaluate side-chains 179 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain W residue 133 ARG Chi-restraints excluded: chain W residue 148 LEU Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 216 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 254 optimal weight: 0.2980 chunk 328 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 349 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN H 39 HIS Y 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.115343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078369 restraints weight = 44564.905| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.58 r_work: 0.3104 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28023 Z= 0.165 Angle : 0.578 8.685 37906 Z= 0.304 Chirality : 0.044 0.182 4348 Planarity : 0.004 0.056 4946 Dihedral : 8.301 158.513 4058 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.18 % Allowed : 10.07 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3598 helix: 2.02 (0.13), residues: 1618 sheet: 0.28 (0.20), residues: 573 loop : 0.01 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 169 TYR 0.018 0.001 TYR D 252 PHE 0.023 0.002 PHE C 456 TRP 0.005 0.001 TRP A 139 HIS 0.005 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00378 (28023) covalent geometry : angle 0.57794 (37906) hydrogen bonds : bond 0.06065 ( 1381) hydrogen bonds : angle 4.65757 ( 3942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6600 (mp-120) REVERT: B 95 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8414 (pp) REVERT: C 231 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: C 407 PHE cc_start: 0.4651 (OUTLIER) cc_final: 0.4357 (m-10) REVERT: C 426 GLN cc_start: 0.7401 (mt0) cc_final: 0.6959 (mt0) REVERT: C 464 LYS cc_start: 0.8558 (mttt) cc_final: 0.7645 (tmtt) REVERT: D 128 ASN cc_start: 0.8139 (m-40) cc_final: 0.7866 (p0) REVERT: D 384 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7844 (mtp) REVERT: D 450 MET cc_start: 0.8778 (mmt) cc_final: 0.8318 (mmm) REVERT: E 61 MET cc_start: 0.9293 (mmt) cc_final: 0.8998 (mmp) REVERT: E 109 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: E 129 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: E 130 LEU cc_start: 0.8986 (tp) cc_final: 0.8726 (tm) REVERT: G 68 MET cc_start: 0.5943 (mtm) cc_final: 0.5695 (mtm) REVERT: G 178 THR cc_start: 0.7987 (m) cc_final: 0.7536 (t) REVERT: H 76 MET cc_start: 0.4150 (ttm) cc_final: 0.3806 (mmm) REVERT: H 77 VAL cc_start: 0.4154 (OUTLIER) cc_final: 0.3943 (p) REVERT: H 122 LEU cc_start: 0.5653 (mm) cc_final: 0.5417 (mt) REVERT: W 133 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.5858 (ttt-90) REVERT: W 158 ASP cc_start: 0.7527 (m-30) cc_final: 0.7263 (m-30) outliers start: 34 outliers final: 17 residues processed: 186 average time/residue: 0.7561 time to fit residues: 160.1849 Evaluate side-chains 182 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain W residue 133 ARG Chi-restraints excluded: chain W residue 148 LEU Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 77 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 250 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS C 458 GLN H 39 HIS X 123 GLN Y 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.116098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079285 restraints weight = 44726.944| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.58 r_work: 0.3125 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28023 Z= 0.130 Angle : 0.534 8.811 37906 Z= 0.280 Chirality : 0.043 0.175 4348 Planarity : 0.004 0.063 4946 Dihedral : 7.957 156.497 4058 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.11 % Allowed : 10.34 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.14), residues: 3598 helix: 2.19 (0.13), residues: 1616 sheet: 0.38 (0.20), residues: 570 loop : 0.06 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 371 TYR 0.019 0.001 TYR D 252 PHE 0.019 0.001 PHE C 456 TRP 0.004 0.001 TRP C 139 HIS 0.004 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00278 (28023) covalent geometry : angle 0.53358 (37906) hydrogen bonds : bond 0.05416 ( 1381) hydrogen bonds : angle 4.52869 ( 3942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6598 (mp-120) REVERT: B 95 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 231 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: C 407 PHE cc_start: 0.4773 (OUTLIER) cc_final: 0.4467 (m-10) REVERT: C 426 GLN cc_start: 0.7428 (mt0) cc_final: 0.7083 (mp10) REVERT: C 440 MET cc_start: 0.8844 (mtp) cc_final: 0.8613 (ttm) REVERT: C 464 LYS cc_start: 0.8530 (mttt) cc_final: 0.7410 (tmtt) REVERT: D 128 ASN cc_start: 0.8120 (m-40) cc_final: 0.7832 (p0) REVERT: D 384 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: D 450 MET cc_start: 0.8739 (mmt) cc_final: 0.8382 (mmm) REVERT: E 61 MET cc_start: 0.9286 (mmt) cc_final: 0.9033 (mmp) REVERT: E 109 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: E 129 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: E 130 LEU cc_start: 0.8946 (tp) cc_final: 0.8699 (tm) REVERT: F 11 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8322 (mtp85) REVERT: G 37 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6669 (mmp) REVERT: G 68 MET cc_start: 0.5932 (mtm) cc_final: 0.5701 (mtm) REVERT: G 178 THR cc_start: 0.7925 (m) cc_final: 0.7477 (t) REVERT: H 76 MET cc_start: 0.4130 (ttm) cc_final: 0.3839 (mmm) REVERT: H 77 VAL cc_start: 0.4191 (OUTLIER) cc_final: 0.3974 (p) REVERT: H 122 LEU cc_start: 0.5605 (mm) cc_final: 0.5370 (mt) REVERT: W 158 ASP cc_start: 0.7534 (m-30) cc_final: 0.7265 (m-30) outliers start: 32 outliers final: 14 residues processed: 191 average time/residue: 0.7722 time to fit residues: 168.9675 Evaluate side-chains 177 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 206 optimal weight: 0.2980 chunk 245 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 279 optimal weight: 0.6980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN H 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.116783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080047 restraints weight = 44820.174| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.58 r_work: 0.3133 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28023 Z= 0.119 Angle : 0.522 9.323 37906 Z= 0.272 Chirality : 0.042 0.167 4348 Planarity : 0.004 0.062 4946 Dihedral : 7.774 154.863 4058 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.94 % Allowed : 10.80 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.14), residues: 3598 helix: 2.26 (0.13), residues: 1625 sheet: 0.40 (0.20), residues: 573 loop : 0.13 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 371 TYR 0.018 0.001 TYR D 252 PHE 0.017 0.001 PHE C 456 TRP 0.004 0.001 TRP C 139 HIS 0.005 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00250 (28023) covalent geometry : angle 0.52199 (37906) hydrogen bonds : bond 0.05137 ( 1381) hydrogen bonds : angle 4.45573 ( 3942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6580 (mp-120) REVERT: A 478 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7261 (ttm-80) REVERT: B 95 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8415 (pp) REVERT: C 231 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: C 407 PHE cc_start: 0.4782 (OUTLIER) cc_final: 0.4493 (m-10) REVERT: C 423 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6858 (pt0) REVERT: C 426 GLN cc_start: 0.7320 (mt0) cc_final: 0.6893 (mp10) REVERT: C 464 LYS cc_start: 0.8333 (mttt) cc_final: 0.7353 (tmtt) REVERT: D 384 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7967 (mtp) REVERT: D 450 MET cc_start: 0.8727 (mmt) cc_final: 0.8370 (mmm) REVERT: E 61 MET cc_start: 0.9263 (mmt) cc_final: 0.8985 (mmp) REVERT: E 109 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: E 129 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: E 130 LEU cc_start: 0.8927 (tp) cc_final: 0.8689 (tm) REVERT: F 11 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8335 (mtp85) REVERT: G 68 MET cc_start: 0.5936 (mtm) cc_final: 0.5704 (mtm) REVERT: G 178 THR cc_start: 0.7940 (m) cc_final: 0.7496 (t) REVERT: H 76 MET cc_start: 0.4177 (ttm) cc_final: 0.3753 (mpp) REVERT: H 77 VAL cc_start: 0.4088 (OUTLIER) cc_final: 0.3851 (p) REVERT: H 122 LEU cc_start: 0.5509 (mm) cc_final: 0.5273 (mt) REVERT: W 158 ASP cc_start: 0.7492 (m-30) cc_final: 0.7185 (m-30) outliers start: 27 outliers final: 13 residues processed: 183 average time/residue: 0.7793 time to fit residues: 161.8735 Evaluate side-chains 177 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 35 optimal weight: 4.9990 chunk 317 optimal weight: 40.0000 chunk 304 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN H 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.116366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079428 restraints weight = 44790.221| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.59 r_work: 0.3123 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28023 Z= 0.132 Angle : 0.542 9.681 37906 Z= 0.283 Chirality : 0.043 0.172 4348 Planarity : 0.004 0.061 4946 Dihedral : 7.819 154.969 4058 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.87 % Allowed : 11.01 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.14), residues: 3598 helix: 2.22 (0.13), residues: 1626 sheet: 0.43 (0.20), residues: 562 loop : 0.09 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 371 TYR 0.018 0.001 TYR D 252 PHE 0.018 0.001 PHE C 456 TRP 0.004 0.001 TRP C 139 HIS 0.006 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00288 (28023) covalent geometry : angle 0.54188 (37906) hydrogen bonds : bond 0.05366 ( 1381) hydrogen bonds : angle 4.47959 ( 3942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7196 Ramachandran restraints generated. 3598 Oldfield, 0 Emsley, 3598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6574 (mp-120) REVERT: A 478 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.7313 (ttm-80) REVERT: B 95 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8406 (pp) REVERT: C 231 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: C 407 PHE cc_start: 0.4803 (OUTLIER) cc_final: 0.4473 (m-10) REVERT: C 426 GLN cc_start: 0.7374 (mt0) cc_final: 0.6994 (mp10) REVERT: C 464 LYS cc_start: 0.8348 (mttt) cc_final: 0.7481 (tttt) REVERT: D 384 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7967 (mtp) REVERT: D 450 MET cc_start: 0.8739 (mmt) cc_final: 0.8378 (mmm) REVERT: E 61 MET cc_start: 0.9265 (mmt) cc_final: 0.8988 (mmp) REVERT: E 109 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: E 129 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: E 130 LEU cc_start: 0.8937 (tp) cc_final: 0.8695 (tm) REVERT: F 11 ARG cc_start: 0.8603 (mtm110) cc_final: 0.8330 (mtp85) REVERT: G 68 MET cc_start: 0.5954 (mtm) cc_final: 0.5721 (mtm) REVERT: G 178 THR cc_start: 0.7940 (m) cc_final: 0.7493 (t) REVERT: H 76 MET cc_start: 0.4098 (ttm) cc_final: 0.3795 (mmm) REVERT: H 77 VAL cc_start: 0.4131 (OUTLIER) cc_final: 0.3904 (p) REVERT: W 158 ASP cc_start: 0.7583 (m-30) cc_final: 0.7318 (m-30) outliers start: 25 outliers final: 14 residues processed: 176 average time/residue: 0.7448 time to fit residues: 149.9163 Evaluate side-chains 175 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain X residue 82 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN H 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.115501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078458 restraints weight = 44349.800| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.59 r_work: 0.3102 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28023 Z= 0.164 Angle : 0.587 10.286 37906 Z= 0.307 Chirality : 0.044 0.175 4348 Planarity : 0.004 0.059 4946 Dihedral : 8.071 157.840 4058 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.87 % Allowed : 11.04 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.14), residues: 3598 helix: 2.10 (0.13), residues: 1628 sheet: 0.36 (0.20), residues: 564 loop : 0.05 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 371 TYR 0.019 0.002 TYR C 401 PHE 0.019 0.002 PHE C 456 TRP 0.006 0.001 TRP G 203 HIS 0.007 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00377 (28023) covalent geometry : angle 0.58700 (37906) hydrogen bonds : bond 0.05894 ( 1381) hydrogen bonds : angle 4.57897 ( 3942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14822.24 seconds wall clock time: 251 minutes 30.81 seconds (15090.81 seconds total)