Starting phenix.real_space_refine on Mon Aug 25 16:51:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vau_31864/08_2025/7vau_31864.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vau_31864/08_2025/7vau_31864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vau_31864/08_2025/7vau_31864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vau_31864/08_2025/7vau_31864.map" model { file = "/net/cci-nas-00/data/ceres_data/7vau_31864/08_2025/7vau_31864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vau_31864/08_2025/7vau_31864.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 5 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18720 2.51 5 N 5125 2.21 5 O 5558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29513 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4466 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 35, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" 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: "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} Time building chain proxies: 5.86, per 1000 atoms: 0.20 Number of scatterers: 29513 At special positions: 0 Unit cell: (137.28, 178.64, 153.12, 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 103 16.00 P 5 15.00 Mg 2 11.99 O 5558 8.00 N 5125 7.00 C 18720 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 928.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6916 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 26 sheets defined 47.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.811A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.410A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.977A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.613A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.124A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.718A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.646A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.796A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.604A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.826A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.507A pdb=" N LEU B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 353 through 364 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.708A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 removed outlier: 3.641A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.524A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 476 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 542 through 550 removed outlier: 4.346A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 558 through 573 removed outlier: 3.604A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.355A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.173A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.512A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.510A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.336A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 533 Processing helix chain 'C' and resid 535 through 541 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.847A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.802A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.574A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.673A pdb=" N SER D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 179' Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.891A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.811A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.813A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.823A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.562A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 removed outlier: 4.018A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.642A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.641A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.694A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.799A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.892A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 457 through 462 removed outlier: 4.005A pdb=" N LYS E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.747A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.585A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.533A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.690A pdb=" N GLU F 230 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.536A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.661A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.530A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 365 removed outlier: 3.532A pdb=" N ASN F 364 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 399 Processing helix chain 'F' and resid 400 through 404 removed outlier: 3.729A pdb=" N ALA F 403 " --> pdb=" O GLY F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.696A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.597A pdb=" N ALA G 112 " --> pdb=" O PRO G 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 109 through 113' Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.813A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 removed outlier: 4.223A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.717A pdb=" N ALA H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 59 " --> pdb=" O PRO H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 59' Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.714A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 106 removed outlier: 3.840A pdb=" N GLU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.866A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 133 Processing helix chain 'J' and resid 170 through 187 removed outlier: 4.119A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 3.771A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.652A pdb=" N ALA L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.537A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.516A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.783A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 5.995A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.565A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP C 43 " --> pdb=" O THR C 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.787A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 45 through 51 removed outlier: 5.893A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR E 54 " --> pdb=" O SER E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 45 through 51 removed outlier: 5.814A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 54 " --> pdb=" O SER F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'J' and resid 162 through 167 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 162 through 167 current: chain 'L' and resid 151 through 155 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 3.828A pdb=" N GLU A 140 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.057A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 383 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.893A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.814A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 148 removed outlier: 3.894A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.788A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 93 Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.013A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.679A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 313 through 315 removed outlier: 5.604A pdb=" N GLN E 338 " --> pdb=" O PRO E 356 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.590A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.527A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE F 313 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU F 257 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N SER F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.552A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 278 through 280 removed outlier: 6.448A pdb=" N TYR F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 93 through 96 Processing sheet with id=AC7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.000A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.174A pdb=" N LEU J 121 " --> pdb=" O LEU J 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 1291 hydrogen bonds defined for protein. 3705 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: 5.48 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9328 1.33 - 1.45: 3589 1.45 - 1.57: 16948 1.57 - 1.69: 8 1.69 - 1.81: 194 Bond restraints: 30067 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.584 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C VAL B 123 " pdb=" N LYS B 124 " ideal model delta sigma weight residual 1.327 1.371 -0.045 1.39e-02 5.18e+03 1.02e+01 bond pdb=" O2B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.470 0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 30062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 40534 3.17 - 6.34: 191 6.34 - 9.51: 13 9.51 - 12.68: 0 12.68 - 15.85: 2 Bond angle restraints: 40740 Sorted by residual: angle pdb=" PA ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 120.50 136.35 -15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 119.90 107.17 12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C GLY B 256 " pdb=" N GLU B 257 " pdb=" CA GLU B 257 " ideal model delta sigma weight residual 121.91 113.61 8.30 2.03e+00 2.43e-01 1.67e+01 angle pdb=" N GLY B 256 " pdb=" CA GLY B 256 " pdb=" C GLY B 256 " ideal model delta sigma weight residual 113.18 104.76 8.42 2.37e+00 1.78e-01 1.26e+01 angle pdb=" CA GLU F 296 " pdb=" C GLU F 296 " pdb=" N ARG F 297 " ideal model delta sigma weight residual 118.27 123.19 -4.92 1.59e+00 3.96e-01 9.57e+00 ... (remaining 40735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 17205 22.47 - 44.94: 997 44.94 - 67.41: 108 67.41 - 89.88: 30 89.88 - 112.35: 2 Dihedral angle restraints: 18342 sinusoidal: 7524 harmonic: 10818 Sorted by residual: dihedral pdb=" CA ALA J 169 " pdb=" C ALA J 169 " pdb=" N ARG J 170 " pdb=" CA ARG J 170 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -172.35 112.35 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" CA LEU J 168 " pdb=" C LEU J 168 " pdb=" N ALA J 169 " pdb=" CA ALA J 169 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 18339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2921 0.041 - 0.082: 1206 0.082 - 0.123: 386 0.123 - 0.164: 52 0.164 - 0.205: 2 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA PHE B 419 " pdb=" N PHE B 419 " pdb=" C PHE B 419 " pdb=" CB PHE B 419 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA GLU D 296 " pdb=" N GLU D 296 " pdb=" C GLU D 296 " pdb=" CB GLU D 296 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 4564 not shown) Planarity restraints: 5329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 394 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 229 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO E 324 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.022 5.00e-02 4.00e+02 ... (remaining 5326 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 170 2.55 - 3.14: 23255 3.14 - 3.73: 44504 3.73 - 4.31: 62372 4.31 - 4.90: 107258 Nonbonded interactions: 237559 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.966 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.967 2.170 nonbonded pdb=" OG SER E 431 " pdb=" OE1 GLU E 434 " model vdw 2.129 3.040 nonbonded pdb=" OE1 GLU F 109 " pdb=" OH TYR F 244 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.162 3.040 ... (remaining 237554 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 1 through 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 through 578)) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 22.680 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 0.007 0.106 30068 Z= 0.316 Angle : 0.686 15.852 40740 Z= 0.362 Chirality : 0.048 0.205 4567 Planarity : 0.005 0.048 5329 Dihedral : 13.704 112.351 11426 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.14), residues: 3761 helix: 1.62 (0.13), residues: 1542 sheet: -0.18 (0.23), residues: 561 loop : -0.10 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 364 TYR 0.025 0.002 TYR D 331 PHE 0.017 0.002 PHE D 418 TRP 0.012 0.002 TRP B 119 HIS 0.007 0.002 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00738 (30067) covalent geometry : angle 0.68649 (40740) hydrogen bonds : bond 0.15462 ( 1291) hydrogen bonds : angle 6.20067 ( 3705) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3710 (mtt) cc_final: 0.3285 (ptm) REVERT: A 20 LEU cc_start: 0.7378 (tp) cc_final: 0.7140 (tp) REVERT: A 29 LYS cc_start: 0.7892 (mmtp) cc_final: 0.7531 (mmmt) REVERT: A 54 ASP cc_start: 0.7649 (t0) cc_final: 0.7231 (t70) REVERT: A 158 LYS cc_start: 0.6661 (mtpt) cc_final: 0.6304 (mttt) REVERT: A 369 ILE cc_start: 0.8782 (mm) cc_final: 0.8438 (mm) REVERT: A 390 ASP cc_start: 0.7731 (t0) cc_final: 0.7519 (t70) REVERT: A 441 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6933 (mm-30) REVERT: A 532 ARG cc_start: 0.6222 (mtm-85) cc_final: 0.5752 (ttp80) REVERT: A 550 ARG cc_start: 0.6793 (tpp-160) cc_final: 0.6279 (mmt90) REVERT: A 556 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6834 (tp30) REVERT: A 568 LYS cc_start: 0.6730 (mtmt) cc_final: 0.6436 (tttt) REVERT: B 133 MET cc_start: 0.7343 (mtp) cc_final: 0.7067 (mtm) REVERT: B 143 PHE cc_start: 0.6081 (t80) cc_final: 0.5590 (m-80) REVERT: B 156 ARG cc_start: 0.6771 (ptm160) cc_final: 0.5999 (ptp90) REVERT: B 338 SER cc_start: 0.8193 (t) cc_final: 0.7735 (m) REVERT: B 342 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7575 (mt-10) REVERT: B 408 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7220 (ttp80) REVERT: B 456 GLU cc_start: 0.7390 (tp30) cc_final: 0.7071 (tp30) REVERT: B 461 GLU cc_start: 0.7666 (tt0) cc_final: 0.7394 (tt0) REVERT: B 469 GLN cc_start: 0.7306 (mt0) cc_final: 0.6988 (tm-30) REVERT: B 481 ARG cc_start: 0.6854 (ttt90) cc_final: 0.6442 (ttp80) REVERT: B 485 GLU cc_start: 0.7125 (tp30) cc_final: 0.6678 (tp30) REVERT: B 498 ASN cc_start: 0.7199 (t0) cc_final: 0.6881 (t0) REVERT: B 517 LYS cc_start: 0.6995 (tppp) cc_final: 0.6698 (tttm) REVERT: B 547 ARG cc_start: 0.6816 (mmm-85) cc_final: 0.6591 (tpp-160) REVERT: C 2 ILE cc_start: 0.8429 (mm) cc_final: 0.8217 (mp) REVERT: C 271 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6550 (tp30) REVERT: C 375 GLU cc_start: 0.7780 (tt0) cc_final: 0.7573 (mt-10) REVERT: C 408 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7435 (ttt-90) REVERT: C 485 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6285 (mm-30) REVERT: D 54 TYR cc_start: 0.8427 (p90) cc_final: 0.8018 (p90) REVERT: D 230 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6734 (mp0) REVERT: D 280 ARG cc_start: 0.6935 (ttt180) cc_final: 0.6617 (ttp80) REVERT: D 394 LYS cc_start: 0.7392 (mttt) cc_final: 0.7029 (mmtt) REVERT: D 466 LYS cc_start: 0.6940 (tttp) cc_final: 0.6664 (tptt) REVERT: E 41 ARG cc_start: 0.6876 (mtp-110) cc_final: 0.6604 (mtp-110) REVERT: E 109 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6941 (tm-30) REVERT: E 216 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7150 (ptp90) REVERT: E 319 ASP cc_start: 0.7875 (m-30) cc_final: 0.7674 (m-30) REVERT: E 448 GLN cc_start: 0.7115 (tt0) cc_final: 0.6902 (tt0) REVERT: E 453 ARG cc_start: 0.6041 (mmt90) cc_final: 0.5666 (mtt90) REVERT: F 6 LYS cc_start: 0.7177 (tttt) cc_final: 0.6695 (tttp) REVERT: F 72 SER cc_start: 0.8895 (p) cc_final: 0.8541 (p) REVERT: F 251 TYR cc_start: 0.8364 (m-80) cc_final: 0.7891 (m-80) REVERT: F 280 ARG cc_start: 0.6714 (mtm180) cc_final: 0.6488 (mtp180) REVERT: F 376 LYS cc_start: 0.7787 (tptp) cc_final: 0.7484 (tttm) REVERT: F 463 TYR cc_start: 0.8483 (t80) cc_final: 0.8280 (t80) REVERT: G 128 ARG cc_start: 0.4854 (mtp180) cc_final: 0.4513 (mtp85) REVERT: G 148 LYS cc_start: 0.6538 (mttp) cc_final: 0.6274 (mmtm) REVERT: G 184 GLU cc_start: 0.7096 (tt0) cc_final: 0.6862 (mm-30) REVERT: H 14 ARG cc_start: 0.5662 (mtm110) cc_final: 0.4866 (mmm-85) REVERT: H 34 GLU cc_start: 0.5420 (mt-10) cc_final: 0.4880 (mm-30) REVERT: H 49 GLU cc_start: 0.3405 (tm-30) cc_final: 0.2956 (tp30) REVERT: I 104 MET cc_start: 0.5917 (mmp) cc_final: 0.5517 (ttp) REVERT: J 81 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6901 (mm-30) REVERT: J 84 ARG cc_start: 0.4668 (ttt180) cc_final: 0.4409 (ttt90) REVERT: J 86 ARG cc_start: 0.5330 (mtt-85) cc_final: 0.4944 (mmm160) REVERT: J 88 ARG cc_start: 0.6302 (ttm-80) cc_final: 0.5814 (ttp-170) REVERT: J 109 LEU cc_start: 0.5486 (mm) cc_final: 0.5229 (mt) REVERT: K 104 MET cc_start: 0.5283 (mmp) cc_final: 0.4623 (ttp) REVERT: K 106 ARG cc_start: 0.4880 (mmp80) cc_final: 0.3416 (ttm110) REVERT: L 81 GLU cc_start: 0.6090 (tp30) cc_final: 0.5790 (tm-30) REVERT: L 106 LYS cc_start: 0.6463 (ptpt) cc_final: 0.5984 (mmtp) REVERT: L 112 LEU cc_start: 0.5794 (mt) cc_final: 0.5581 (mt) outliers start: 0 outliers final: 0 residues processed: 623 average time/residue: 0.2180 time to fit residues: 199.8026 Evaluate side-chains 352 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 423 ASN C 316 GLN C 477 GLN E 310 GLN E 364 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107910 restraints weight = 47062.718| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.58 r_work: 0.3207 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30068 Z= 0.118 Angle : 0.528 7.915 40740 Z= 0.271 Chirality : 0.043 0.143 4567 Planarity : 0.004 0.045 5329 Dihedral : 5.262 102.910 4223 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.88 % Allowed : 6.59 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.14), residues: 3761 helix: 1.95 (0.14), residues: 1537 sheet: -0.21 (0.23), residues: 563 loop : 0.09 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 416 TYR 0.013 0.001 TYR D 331 PHE 0.022 0.001 PHE H 81 TRP 0.013 0.001 TRP D 471 HIS 0.004 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00248 (30067) covalent geometry : angle 0.52831 (40740) hydrogen bonds : bond 0.05023 ( 1291) hydrogen bonds : angle 4.74029 ( 3705) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 411 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4580 (mtt) cc_final: 0.3854 (ptm) REVERT: A 29 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7934 (mmtt) REVERT: A 54 ASP cc_start: 0.7859 (t0) cc_final: 0.7543 (t70) REVERT: A 98 THR cc_start: 0.8007 (m) cc_final: 0.7531 (p) REVERT: A 159 GLU cc_start: 0.6974 (pp20) cc_final: 0.6583 (pp20) REVERT: A 241 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 369 ILE cc_start: 0.8620 (mm) cc_final: 0.8371 (mm) REVERT: A 390 ASP cc_start: 0.8081 (t0) cc_final: 0.7795 (t70) REVERT: A 441 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7424 (tt0) REVERT: A 532 ARG cc_start: 0.6628 (mtm-85) cc_final: 0.6247 (ttp80) REVERT: A 550 ARG cc_start: 0.6900 (tpp-160) cc_final: 0.6633 (mmt180) REVERT: A 565 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6367 (pt0) REVERT: A 568 LYS cc_start: 0.7004 (mtmt) cc_final: 0.6686 (tttt) REVERT: B 143 PHE cc_start: 0.6025 (t80) cc_final: 0.5548 (m-80) REVERT: B 156 ARG cc_start: 0.7068 (ptm160) cc_final: 0.6377 (ptp90) REVERT: B 338 SER cc_start: 0.8721 (t) cc_final: 0.8269 (m) REVERT: B 342 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 408 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7865 (ttp80) REVERT: B 461 GLU cc_start: 0.7797 (tt0) cc_final: 0.7507 (tt0) REVERT: B 469 GLN cc_start: 0.7662 (mt0) cc_final: 0.7378 (tm-30) REVERT: B 485 GLU cc_start: 0.7535 (tp30) cc_final: 0.7040 (tp30) REVERT: B 547 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.7035 (tpp-160) REVERT: C 8 LYS cc_start: 0.8900 (tttt) cc_final: 0.8653 (tttm) REVERT: C 130 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6879 (ttm-80) REVERT: C 271 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6786 (tp30) REVERT: D 54 TYR cc_start: 0.8453 (p90) cc_final: 0.8010 (p90) REVERT: D 230 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7306 (mp0) REVERT: D 394 LYS cc_start: 0.7816 (mttt) cc_final: 0.7587 (mmtt) REVERT: E 41 ARG cc_start: 0.7327 (mtp-110) cc_final: 0.7056 (mtp-110) REVERT: E 412 LEU cc_start: 0.8172 (tp) cc_final: 0.7821 (tt) REVERT: F 6 LYS cc_start: 0.7421 (tttt) cc_final: 0.7180 (tttp) REVERT: G 128 ARG cc_start: 0.4962 (mtp180) cc_final: 0.4606 (mtp85) REVERT: G 148 LYS cc_start: 0.7370 (mttp) cc_final: 0.7002 (mmtm) REVERT: H 14 ARG cc_start: 0.5721 (mtm110) cc_final: 0.4981 (mmm-85) REVERT: H 34 GLU cc_start: 0.5494 (mt-10) cc_final: 0.5123 (mm-30) REVERT: H 49 GLU cc_start: 0.3883 (tm-30) cc_final: 0.3305 (tp30) REVERT: H 59 VAL cc_start: 0.6060 (m) cc_final: 0.5815 (p) REVERT: H 87 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6295 (tm-30) REVERT: I 104 MET cc_start: 0.5966 (mmp) cc_final: 0.5641 (ttp) REVERT: J 74 GLN cc_start: 0.7199 (tp40) cc_final: 0.6892 (tt0) REVERT: J 81 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7341 (mm-30) REVERT: J 84 ARG cc_start: 0.5421 (ttt180) cc_final: 0.5064 (ttt-90) REVERT: J 88 ARG cc_start: 0.6374 (ttm-80) cc_final: 0.6120 (ttp-170) REVERT: J 109 LEU cc_start: 0.5685 (mm) cc_final: 0.5410 (mt) REVERT: K 104 MET cc_start: 0.5320 (mmp) cc_final: 0.4614 (ttp) REVERT: K 106 ARG cc_start: 0.4912 (mmp80) cc_final: 0.3545 (ttm110) REVERT: L 106 LYS cc_start: 0.6692 (ptpt) cc_final: 0.6013 (mmtp) outliers start: 27 outliers final: 18 residues processed: 430 average time/residue: 0.2147 time to fit residues: 137.6164 Evaluate side-chains 347 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 328 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain G residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 199 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 315 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 ASN C 316 GLN ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN E 310 GLN E 448 GLN F 23 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101611 restraints weight = 48006.931| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.68 r_work: 0.3108 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 30068 Z= 0.346 Angle : 0.769 9.135 40740 Z= 0.395 Chirality : 0.053 0.242 4567 Planarity : 0.007 0.081 5329 Dihedral : 5.967 84.537 4223 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.98 % Allowed : 11.39 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.13), residues: 3761 helix: 1.03 (0.13), residues: 1550 sheet: -0.56 (0.22), residues: 568 loop : -0.55 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 491 TYR 0.025 0.003 TYR F 331 PHE 0.025 0.003 PHE G 70 TRP 0.015 0.003 TRP J 175 HIS 0.008 0.002 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00864 (30067) covalent geometry : angle 0.76939 (40740) hydrogen bonds : bond 0.06921 ( 1291) hydrogen bonds : angle 5.12957 ( 3705) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 323 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4477 (mtt) cc_final: 0.3596 (ptm) REVERT: A 20 LEU cc_start: 0.7592 (tp) cc_final: 0.7348 (tp) REVERT: A 54 ASP cc_start: 0.8187 (t0) cc_final: 0.7927 (t70) REVERT: A 98 THR cc_start: 0.8068 (m) cc_final: 0.7632 (p) REVERT: A 241 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7972 (mp) REVERT: A 550 ARG cc_start: 0.6999 (tpp-160) cc_final: 0.6585 (mmt90) REVERT: A 568 LYS cc_start: 0.7206 (mtmt) cc_final: 0.6856 (tttt) REVERT: B 143 PHE cc_start: 0.6465 (t80) cc_final: 0.6094 (m-80) REVERT: B 156 ARG cc_start: 0.7191 (ptm160) cc_final: 0.6498 (ptp90) REVERT: B 209 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7833 (mtm) REVERT: B 338 SER cc_start: 0.8933 (t) cc_final: 0.8511 (m) REVERT: B 342 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7938 (mt-10) REVERT: B 408 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.8002 (ttp80) REVERT: B 410 ASP cc_start: 0.7324 (t0) cc_final: 0.7108 (t0) REVERT: B 469 GLN cc_start: 0.7834 (mt0) cc_final: 0.7427 (pp30) REVERT: B 481 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7647 (ttp80) REVERT: B 482 LEU cc_start: 0.8189 (tp) cc_final: 0.7955 (tt) REVERT: C 45 ASP cc_start: 0.8266 (p0) cc_final: 0.8061 (t0) REVERT: C 130 ARG cc_start: 0.7157 (mtt90) cc_final: 0.6853 (ttm-80) REVERT: C 271 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6968 (tp30) REVERT: C 485 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7087 (mm-30) REVERT: D 368 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7434 (ptmt) REVERT: D 394 LYS cc_start: 0.8156 (mttt) cc_final: 0.7836 (mmtt) REVERT: E 61 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7088 (mt-10) REVERT: E 311 ILE cc_start: 0.8749 (pt) cc_final: 0.8533 (mt) REVERT: E 364 ASN cc_start: 0.7745 (m-40) cc_final: 0.7541 (m110) REVERT: F 6 LYS cc_start: 0.7764 (tttt) cc_final: 0.7497 (tttp) REVERT: F 376 LYS cc_start: 0.8540 (tptp) cc_final: 0.8292 (tttm) REVERT: G 148 LYS cc_start: 0.7629 (mttp) cc_final: 0.7205 (mmtm) REVERT: H 14 ARG cc_start: 0.6000 (mtm110) cc_final: 0.5189 (mmm-85) REVERT: H 34 GLU cc_start: 0.5605 (mt-10) cc_final: 0.5316 (mm-30) REVERT: I 104 MET cc_start: 0.6013 (mmp) cc_final: 0.5659 (ttp) REVERT: J 74 GLN cc_start: 0.7403 (tp40) cc_final: 0.6909 (tt0) REVERT: J 81 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7231 (mm-30) REVERT: J 88 ARG cc_start: 0.6559 (ttm-80) cc_final: 0.6298 (ttp-170) REVERT: J 109 LEU cc_start: 0.5881 (mm) cc_final: 0.5532 (mt) REVERT: J 119 LYS cc_start: 0.6559 (tptp) cc_final: 0.5976 (ptmt) REVERT: K 104 MET cc_start: 0.5573 (mmp) cc_final: 0.4841 (ttp) REVERT: K 106 ARG cc_start: 0.4933 (mmp80) cc_final: 0.3316 (ttm-80) REVERT: L 106 LYS cc_start: 0.6722 (ptpt) cc_final: 0.6090 (mmtp) outliers start: 61 outliers final: 39 residues processed: 364 average time/residue: 0.2057 time to fit residues: 113.9016 Evaluate side-chains 340 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 312 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 294 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 GLN C 316 GLN C 418 HIS F 23 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108058 restraints weight = 46893.418| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.47 r_work: 0.3209 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30068 Z= 0.103 Angle : 0.501 7.418 40740 Z= 0.256 Chirality : 0.042 0.152 4567 Planarity : 0.004 0.048 5329 Dihedral : 5.185 86.472 4223 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.43 % Allowed : 12.72 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.14), residues: 3761 helix: 1.66 (0.14), residues: 1545 sheet: -0.39 (0.22), residues: 551 loop : -0.22 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 41 TYR 0.012 0.001 TYR H 89 PHE 0.020 0.001 PHE H 81 TRP 0.017 0.001 TRP A 119 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00216 (30067) covalent geometry : angle 0.50134 (40740) hydrogen bonds : bond 0.04447 ( 1291) hydrogen bonds : angle 4.53256 ( 3705) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 334 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4410 (mtt) cc_final: 0.3609 (ptm) REVERT: A 29 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7956 (mmmm) REVERT: A 45 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8044 (t0) REVERT: A 54 ASP cc_start: 0.8020 (t0) cc_final: 0.7684 (t70) REVERT: A 97 LYS cc_start: 0.6868 (mtpt) cc_final: 0.6135 (mmtm) REVERT: A 98 THR cc_start: 0.8013 (m) cc_final: 0.7579 (p) REVERT: A 241 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 374 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: A 568 LYS cc_start: 0.7027 (mtmt) cc_final: 0.6674 (tttt) REVERT: B 156 ARG cc_start: 0.7216 (ptm160) cc_final: 0.6464 (ptp90) REVERT: B 338 SER cc_start: 0.8853 (t) cc_final: 0.8384 (m) REVERT: B 342 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 408 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7865 (ttp80) REVERT: B 410 ASP cc_start: 0.7253 (t0) cc_final: 0.6974 (t0) REVERT: B 469 GLN cc_start: 0.7630 (mt0) cc_final: 0.7259 (pp30) REVERT: C 8 LYS cc_start: 0.8922 (tttt) cc_final: 0.8636 (tttm) REVERT: C 130 ARG cc_start: 0.7161 (mtt90) cc_final: 0.6735 (ttm-80) REVERT: C 271 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6821 (tp30) REVERT: D 230 GLU cc_start: 0.8190 (mp0) cc_final: 0.7846 (mp0) REVERT: D 368 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7353 (ptmt) REVERT: D 394 LYS cc_start: 0.7759 (mttt) cc_final: 0.7483 (mmtt) REVERT: E 311 ILE cc_start: 0.8564 (pt) cc_final: 0.8272 (mt) REVERT: F 6 LYS cc_start: 0.7641 (tttt) cc_final: 0.7405 (tttp) REVERT: F 334 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: F 405 THR cc_start: 0.6385 (OUTLIER) cc_final: 0.6115 (m) REVERT: G 51 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.5802 (mmtm) REVERT: G 148 LYS cc_start: 0.7373 (mttp) cc_final: 0.7002 (mmtm) REVERT: H 14 ARG cc_start: 0.5844 (mtm110) cc_final: 0.5055 (mmm-85) REVERT: H 34 GLU cc_start: 0.5574 (mt-10) cc_final: 0.5296 (mm-30) REVERT: H 49 GLU cc_start: 0.3985 (tm-30) cc_final: 0.3335 (tp30) REVERT: H 87 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6094 (mm-30) REVERT: I 87 ARG cc_start: 0.5749 (ptm-80) cc_final: 0.5411 (ptm-80) REVERT: J 74 GLN cc_start: 0.7249 (tp40) cc_final: 0.6924 (tt0) REVERT: J 81 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7325 (mm-30) REVERT: J 109 LEU cc_start: 0.5801 (mm) cc_final: 0.5489 (mt) REVERT: K 104 MET cc_start: 0.5458 (mmp) cc_final: 0.4772 (ttp) REVERT: K 106 ARG cc_start: 0.4733 (mmp80) cc_final: 0.3419 (ttm-80) REVERT: L 106 LYS cc_start: 0.6734 (ptpt) cc_final: 0.6029 (mmtp) outliers start: 44 outliers final: 23 residues processed: 363 average time/residue: 0.2091 time to fit residues: 114.2241 Evaluate side-chains 334 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 303 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 15 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 354 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 364 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102233 restraints weight = 47774.828| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.56 r_work: 0.3120 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 30068 Z= 0.296 Angle : 0.698 9.675 40740 Z= 0.357 Chirality : 0.050 0.229 4567 Planarity : 0.006 0.066 5329 Dihedral : 5.771 88.130 4223 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.43 % Allowed : 14.34 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.13), residues: 3761 helix: 1.09 (0.13), residues: 1558 sheet: -0.69 (0.22), residues: 568 loop : -0.64 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 360 TYR 0.021 0.002 TYR F 331 PHE 0.025 0.003 PHE G 70 TRP 0.016 0.002 TRP A 119 HIS 0.006 0.002 HIS D 458 Details of bonding type rmsd covalent geometry : bond 0.00728 (30067) covalent geometry : angle 0.69845 (40740) hydrogen bonds : bond 0.06310 ( 1291) hydrogen bonds : angle 4.94081 ( 3705) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4482 (mtt) cc_final: 0.3620 (ptm) REVERT: A 20 LEU cc_start: 0.7651 (tp) cc_final: 0.7404 (tp) REVERT: A 45 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8158 (t70) REVERT: A 97 LYS cc_start: 0.7020 (mtpt) cc_final: 0.6267 (mmtm) REVERT: A 98 THR cc_start: 0.8062 (m) cc_final: 0.7637 (p) REVERT: A 119 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.8299 (t-100) REVERT: A 241 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 568 LYS cc_start: 0.7193 (mtmt) cc_final: 0.6844 (tttt) REVERT: B 24 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8425 (tpp) REVERT: B 85 ASP cc_start: 0.7915 (p0) cc_final: 0.7568 (p0) REVERT: B 156 ARG cc_start: 0.7225 (ptm160) cc_final: 0.6495 (ptp90) REVERT: B 338 SER cc_start: 0.8942 (t) cc_final: 0.8510 (m) REVERT: B 408 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7980 (ttp80) REVERT: B 410 ASP cc_start: 0.7353 (t0) cc_final: 0.7142 (t0) REVERT: B 469 GLN cc_start: 0.7791 (mt0) cc_final: 0.7408 (pp30) REVERT: B 481 ARG cc_start: 0.7899 (ttt90) cc_final: 0.7645 (ttp80) REVERT: B 482 LEU cc_start: 0.8188 (tp) cc_final: 0.7942 (tt) REVERT: B 547 ARG cc_start: 0.8238 (tpp-160) cc_final: 0.7982 (tpp-160) REVERT: C 130 ARG cc_start: 0.7155 (mtt90) cc_final: 0.6850 (ttm-80) REVERT: C 271 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7010 (tp30) REVERT: C 524 LYS cc_start: 0.8257 (tttm) cc_final: 0.7994 (ttmt) REVERT: D 230 GLU cc_start: 0.8371 (mp0) cc_final: 0.7955 (mp0) REVERT: D 368 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.6868 (ptmt) REVERT: D 394 LYS cc_start: 0.8114 (mttt) cc_final: 0.7697 (mmtt) REVERT: E 61 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7029 (mt-10) REVERT: F 6 LYS cc_start: 0.7898 (tttt) cc_final: 0.7575 (tttp) REVERT: F 376 LYS cc_start: 0.8508 (tptp) cc_final: 0.8298 (tttm) REVERT: H 1 MET cc_start: 0.5890 (tpp) cc_final: 0.5619 (tpp) REVERT: H 14 ARG cc_start: 0.5995 (mtm110) cc_final: 0.5183 (mmm-85) REVERT: H 34 GLU cc_start: 0.5639 (mt-10) cc_final: 0.5345 (mm-30) REVERT: H 87 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6187 (mm-30) REVERT: J 74 GLN cc_start: 0.7326 (tp40) cc_final: 0.6880 (tt0) REVERT: J 81 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7234 (mm-30) REVERT: J 109 LEU cc_start: 0.5978 (mm) cc_final: 0.5637 (mt) REVERT: J 119 LYS cc_start: 0.6544 (tptp) cc_final: 0.6061 (ptmt) REVERT: K 104 MET cc_start: 0.5584 (mmp) cc_final: 0.4864 (ttp) REVERT: K 106 ARG cc_start: 0.4928 (mmp80) cc_final: 0.3608 (ttp-110) REVERT: L 106 LYS cc_start: 0.6664 (ptpt) cc_final: 0.6009 (mmtp) outliers start: 75 outliers final: 46 residues processed: 361 average time/residue: 0.2042 time to fit residues: 112.3656 Evaluate side-chains 340 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 355 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 357 optimal weight: 20.0000 chunk 364 optimal weight: 4.9990 chunk 329 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104694 restraints weight = 47474.535| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.53 r_work: 0.3171 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30068 Z= 0.170 Angle : 0.567 7.843 40740 Z= 0.289 Chirality : 0.045 0.214 4567 Planarity : 0.005 0.048 5329 Dihedral : 5.487 89.160 4223 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.53 % Allowed : 14.89 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.14), residues: 3761 helix: 1.33 (0.13), residues: 1545 sheet: -0.67 (0.22), residues: 538 loop : -0.59 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 360 TYR 0.014 0.001 TYR C 428 PHE 0.017 0.002 PHE H 81 TRP 0.016 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00406 (30067) covalent geometry : angle 0.56705 (40740) hydrogen bonds : bond 0.05226 ( 1291) hydrogen bonds : angle 4.70634 ( 3705) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 298 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4273 (mtt) cc_final: 0.3477 (ptm) REVERT: A 45 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8128 (t0) REVERT: A 54 ASP cc_start: 0.8119 (t0) cc_final: 0.7832 (t70) REVERT: A 97 LYS cc_start: 0.6934 (mtpt) cc_final: 0.6131 (mmtm) REVERT: A 98 THR cc_start: 0.8061 (m) cc_final: 0.7656 (p) REVERT: A 119 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.8243 (t-100) REVERT: A 241 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7814 (mp) REVERT: A 257 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6382 (tt0) REVERT: A 568 LYS cc_start: 0.7122 (mtmt) cc_final: 0.6767 (tttt) REVERT: B 85 ASP cc_start: 0.7711 (p0) cc_final: 0.7507 (p0) REVERT: B 156 ARG cc_start: 0.7215 (ptm160) cc_final: 0.6461 (ptp90) REVERT: B 338 SER cc_start: 0.8861 (t) cc_final: 0.8398 (m) REVERT: B 342 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7876 (mt-10) REVERT: B 408 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7866 (ttp80) REVERT: B 410 ASP cc_start: 0.7392 (t0) cc_final: 0.7132 (t0) REVERT: B 469 GLN cc_start: 0.7686 (mt0) cc_final: 0.7318 (pp30) REVERT: B 481 ARG cc_start: 0.7698 (ttt90) cc_final: 0.7471 (ttp80) REVERT: B 482 LEU cc_start: 0.8067 (tp) cc_final: 0.7829 (tt) REVERT: B 547 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7931 (tpp-160) REVERT: C 130 ARG cc_start: 0.7098 (mtt90) cc_final: 0.6768 (ttm-80) REVERT: C 271 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6977 (tp30) REVERT: C 524 LYS cc_start: 0.8152 (tttm) cc_final: 0.7892 (ttmt) REVERT: D 368 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6883 (ptmt) REVERT: D 394 LYS cc_start: 0.7950 (mttt) cc_final: 0.7538 (mmtt) REVERT: F 6 LYS cc_start: 0.7844 (tttt) cc_final: 0.7473 (tttp) REVERT: G 148 LYS cc_start: 0.7518 (mttp) cc_final: 0.7064 (mmtm) REVERT: H 14 ARG cc_start: 0.5927 (mtm110) cc_final: 0.5142 (mmm-85) REVERT: H 34 GLU cc_start: 0.5616 (mt-10) cc_final: 0.5370 (mm-30) REVERT: H 87 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6099 (mm-30) REVERT: H 89 TYR cc_start: 0.6180 (t80) cc_final: 0.5950 (t80) REVERT: I 87 ARG cc_start: 0.5917 (ptm-80) cc_final: 0.5450 (ptm-80) REVERT: I 104 MET cc_start: 0.6163 (ttt) cc_final: 0.5864 (ttm) REVERT: J 74 GLN cc_start: 0.7270 (tp40) cc_final: 0.6903 (tt0) REVERT: J 81 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7120 (mm-30) REVERT: J 109 LEU cc_start: 0.5952 (mm) cc_final: 0.5641 (mt) REVERT: K 104 MET cc_start: 0.5540 (mmp) cc_final: 0.5031 (mtp) REVERT: K 106 ARG cc_start: 0.5005 (mmp80) cc_final: 0.3488 (ttm-80) REVERT: L 106 LYS cc_start: 0.6596 (ptpt) cc_final: 0.5888 (mmtp) REVERT: L 141 GLU cc_start: 0.5442 (OUTLIER) cc_final: 0.4252 (tm-30) outliers start: 78 outliers final: 55 residues processed: 358 average time/residue: 0.1967 time to fit residues: 108.6099 Evaluate side-chains 345 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 283 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 6 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 201 optimal weight: 0.6980 chunk 166 optimal weight: 9.9990 chunk 287 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN C 316 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103604 restraints weight = 47744.730| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.52 r_work: 0.3155 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30068 Z= 0.224 Angle : 0.629 11.795 40740 Z= 0.320 Chirality : 0.047 0.244 4567 Planarity : 0.006 0.052 5329 Dihedral : 5.638 88.228 4223 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.15 % Allowed : 15.12 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.13), residues: 3761 helix: 1.17 (0.13), residues: 1549 sheet: -0.77 (0.23), residues: 538 loop : -0.75 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 41 TYR 0.018 0.002 TYR C 428 PHE 0.018 0.002 PHE G 70 TRP 0.016 0.002 TRP A 119 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00547 (30067) covalent geometry : angle 0.62890 (40740) hydrogen bonds : bond 0.05705 ( 1291) hydrogen bonds : angle 4.80530 ( 3705) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 292 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4409 (mtt) cc_final: 0.3701 (ptm) REVERT: A 45 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8116 (t0) REVERT: A 97 LYS cc_start: 0.6977 (mtpt) cc_final: 0.6166 (mmtm) REVERT: A 98 THR cc_start: 0.8011 (m) cc_final: 0.7572 (p) REVERT: A 119 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.8274 (t-100) REVERT: A 241 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 257 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6424 (tt0) REVERT: A 568 LYS cc_start: 0.7159 (mtmt) cc_final: 0.6820 (tttt) REVERT: B 85 ASP cc_start: 0.7706 (p0) cc_final: 0.7377 (p0) REVERT: B 156 ARG cc_start: 0.7090 (ptm160) cc_final: 0.6769 (ttp-110) REVERT: B 338 SER cc_start: 0.8886 (t) cc_final: 0.8369 (m) REVERT: B 408 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7885 (ttp80) REVERT: B 410 ASP cc_start: 0.7511 (t0) cc_final: 0.7270 (t0) REVERT: B 449 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7944 (mt-10) REVERT: B 469 GLN cc_start: 0.7683 (mt0) cc_final: 0.7291 (pp30) REVERT: B 481 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7562 (ttp80) REVERT: B 482 LEU cc_start: 0.8137 (tp) cc_final: 0.7895 (tt) REVERT: B 547 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7894 (tpp-160) REVERT: B 558 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5575 (tp30) REVERT: C 130 ARG cc_start: 0.7071 (mtt90) cc_final: 0.6737 (ttm-80) REVERT: C 271 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7001 (tp30) REVERT: C 524 LYS cc_start: 0.8159 (tttm) cc_final: 0.7906 (ttmt) REVERT: D 206 GLN cc_start: 0.7508 (mt0) cc_final: 0.7209 (tm-30) REVERT: D 368 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6872 (ptmt) REVERT: D 394 LYS cc_start: 0.7878 (mttt) cc_final: 0.7529 (mmtt) REVERT: E 318 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: F 6 LYS cc_start: 0.7887 (tttt) cc_final: 0.7498 (tttp) REVERT: G 148 LYS cc_start: 0.7523 (mttp) cc_final: 0.7071 (mmtm) REVERT: H 1 MET cc_start: 0.5791 (tpp) cc_final: 0.5525 (tpp) REVERT: H 14 ARG cc_start: 0.6095 (mtm110) cc_final: 0.5321 (mmm-85) REVERT: H 34 GLU cc_start: 0.5655 (mt-10) cc_final: 0.5389 (mm-30) REVERT: H 87 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6203 (mm-30) REVERT: I 104 MET cc_start: 0.6122 (ttt) cc_final: 0.5806 (ttm) REVERT: J 81 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7095 (mm-30) REVERT: J 109 LEU cc_start: 0.5956 (mm) cc_final: 0.5610 (mt) REVERT: K 104 MET cc_start: 0.5687 (mmp) cc_final: 0.5179 (mtp) REVERT: K 106 ARG cc_start: 0.5057 (mmp80) cc_final: 0.3412 (ttm-80) REVERT: L 106 LYS cc_start: 0.6562 (ptpt) cc_final: 0.5935 (mmtp) REVERT: L 141 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.4254 (tm-30) outliers start: 97 outliers final: 62 residues processed: 365 average time/residue: 0.1863 time to fit residues: 105.1120 Evaluate side-chains 351 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 280 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 117 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 372 optimal weight: 20.0000 chunk 295 optimal weight: 4.9990 chunk 217 optimal weight: 0.0020 chunk 36 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104383 restraints weight = 47423.306| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.54 r_work: 0.3160 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30068 Z= 0.146 Angle : 0.548 9.879 40740 Z= 0.279 Chirality : 0.044 0.244 4567 Planarity : 0.005 0.047 5329 Dihedral : 5.360 87.709 4223 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.66 % Allowed : 15.70 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.14), residues: 3761 helix: 1.43 (0.13), residues: 1539 sheet: -0.69 (0.23), residues: 538 loop : -0.60 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 41 TYR 0.013 0.001 TYR C 428 PHE 0.017 0.001 PHE H 81 TRP 0.016 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00345 (30067) covalent geometry : angle 0.54764 (40740) hydrogen bonds : bond 0.04911 ( 1291) hydrogen bonds : angle 4.61003 ( 3705) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 292 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4641 (mtt) cc_final: 0.3858 (ptm) REVERT: A 54 ASP cc_start: 0.8137 (t0) cc_final: 0.7841 (t70) REVERT: A 97 LYS cc_start: 0.6934 (mtpt) cc_final: 0.6138 (mmtm) REVERT: A 98 THR cc_start: 0.7964 (m) cc_final: 0.7550 (p) REVERT: A 257 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: A 555 SER cc_start: 0.7343 (OUTLIER) cc_final: 0.6857 (p) REVERT: A 568 LYS cc_start: 0.7183 (mtmt) cc_final: 0.6843 (tttt) REVERT: B 156 ARG cc_start: 0.7147 (ptm160) cc_final: 0.6847 (ttp-110) REVERT: B 338 SER cc_start: 0.8928 (t) cc_final: 0.8429 (m) REVERT: B 408 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7969 (ttp80) REVERT: B 410 ASP cc_start: 0.7482 (t0) cc_final: 0.7254 (t0) REVERT: B 449 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7965 (mt-10) REVERT: B 469 GLN cc_start: 0.7739 (mt0) cc_final: 0.7418 (pp30) REVERT: B 481 ARG cc_start: 0.7895 (ttt90) cc_final: 0.7620 (ttp80) REVERT: B 482 LEU cc_start: 0.8131 (tp) cc_final: 0.7878 (tt) REVERT: B 547 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7916 (tpp-160) REVERT: B 558 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5628 (tp30) REVERT: C 130 ARG cc_start: 0.7102 (mtt90) cc_final: 0.6797 (ttm-80) REVERT: C 271 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6913 (tp30) REVERT: C 524 LYS cc_start: 0.8185 (tttm) cc_final: 0.7931 (ttmt) REVERT: D 206 GLN cc_start: 0.7504 (mt0) cc_final: 0.7302 (tm-30) REVERT: D 368 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.6819 (ptmt) REVERT: D 394 LYS cc_start: 0.7905 (mttt) cc_final: 0.7557 (mmtt) REVERT: E 318 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: F 6 LYS cc_start: 0.7922 (tttt) cc_final: 0.7582 (tttp) REVERT: G 148 LYS cc_start: 0.7640 (mttp) cc_final: 0.7180 (mmtm) REVERT: H 1 MET cc_start: 0.5904 (tpp) cc_final: 0.5637 (tpp) REVERT: H 14 ARG cc_start: 0.5947 (mtm110) cc_final: 0.5215 (mmm-85) REVERT: H 34 GLU cc_start: 0.5610 (mt-10) cc_final: 0.5219 (mm-30) REVERT: H 87 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6212 (mm-30) REVERT: I 104 MET cc_start: 0.6180 (ttt) cc_final: 0.5864 (ttm) REVERT: J 74 GLN cc_start: 0.7236 (tp40) cc_final: 0.6909 (tt0) REVERT: J 81 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7373 (tt0) REVERT: J 109 LEU cc_start: 0.5978 (mm) cc_final: 0.5698 (mt) REVERT: K 104 MET cc_start: 0.5650 (mmp) cc_final: 0.5145 (mtp) REVERT: K 106 ARG cc_start: 0.4998 (mmp80) cc_final: 0.3593 (ttm-80) REVERT: L 106 LYS cc_start: 0.6642 (ptpt) cc_final: 0.5969 (mmtp) REVERT: L 141 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.4314 (tm-30) outliers start: 82 outliers final: 59 residues processed: 353 average time/residue: 0.1978 time to fit residues: 107.2332 Evaluate side-chains 347 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 281 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 62 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 356 optimal weight: 9.9990 chunk 207 optimal weight: 0.0170 chunk 11 optimal weight: 9.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN F 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105984 restraints weight = 47310.427| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.53 r_work: 0.3189 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30068 Z= 0.129 Angle : 0.532 9.565 40740 Z= 0.269 Chirality : 0.043 0.267 4567 Planarity : 0.005 0.046 5329 Dihedral : 5.191 86.883 4223 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.43 % Allowed : 15.90 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.14), residues: 3761 helix: 1.59 (0.14), residues: 1539 sheet: -0.65 (0.23), residues: 533 loop : -0.51 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 284 TYR 0.012 0.001 TYR C 428 PHE 0.018 0.001 PHE H 81 TRP 0.018 0.001 TRP A 119 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00299 (30067) covalent geometry : angle 0.53195 (40740) hydrogen bonds : bond 0.04607 ( 1291) hydrogen bonds : angle 4.51032 ( 3705) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 296 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4572 (mtt) cc_final: 0.4091 (ptm) REVERT: A 54 ASP cc_start: 0.8073 (t0) cc_final: 0.7763 (t70) REVERT: A 97 LYS cc_start: 0.6882 (mtpt) cc_final: 0.6072 (mmtm) REVERT: A 98 THR cc_start: 0.7957 (m) cc_final: 0.7533 (p) REVERT: A 241 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7766 (mp) REVERT: A 257 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6268 (mt-10) REVERT: A 555 SER cc_start: 0.7407 (OUTLIER) cc_final: 0.6866 (p) REVERT: A 568 LYS cc_start: 0.7080 (mtmt) cc_final: 0.6714 (tttt) REVERT: B 156 ARG cc_start: 0.7079 (ptm160) cc_final: 0.6757 (ttp-110) REVERT: B 338 SER cc_start: 0.8861 (t) cc_final: 0.8329 (m) REVERT: B 408 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7881 (ttp80) REVERT: B 410 ASP cc_start: 0.7439 (t0) cc_final: 0.7187 (t0) REVERT: B 449 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7876 (mt-10) REVERT: B 469 GLN cc_start: 0.7636 (mt0) cc_final: 0.7346 (pp30) REVERT: B 481 ARG cc_start: 0.7732 (ttt90) cc_final: 0.7433 (ttp80) REVERT: B 482 LEU cc_start: 0.8072 (tp) cc_final: 0.7843 (tt) REVERT: B 547 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7865 (tpp-160) REVERT: B 558 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.5498 (tp30) REVERT: C 8 LYS cc_start: 0.8895 (tttt) cc_final: 0.8571 (tttm) REVERT: C 130 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6696 (ttm-80) REVERT: C 271 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6874 (tp30) REVERT: C 524 LYS cc_start: 0.8008 (tttm) cc_final: 0.7766 (ttmt) REVERT: D 206 GLN cc_start: 0.7418 (mt0) cc_final: 0.7206 (tm-30) REVERT: D 349 TYR cc_start: 0.8487 (t80) cc_final: 0.8183 (t80) REVERT: D 368 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.6897 (ptmt) REVERT: D 394 LYS cc_start: 0.7807 (mttt) cc_final: 0.7419 (mmtt) REVERT: E 41 ARG cc_start: 0.7421 (mtp-110) cc_final: 0.7176 (mtp-110) REVERT: F 6 LYS cc_start: 0.7820 (tttt) cc_final: 0.7476 (tttp) REVERT: G 148 LYS cc_start: 0.7409 (mttp) cc_final: 0.7028 (mmtm) REVERT: H 14 ARG cc_start: 0.5920 (mtm110) cc_final: 0.5171 (mmm-85) REVERT: H 34 GLU cc_start: 0.5598 (mt-10) cc_final: 0.5230 (mm-30) REVERT: H 47 VAL cc_start: 0.6896 (OUTLIER) cc_final: 0.6396 (p) REVERT: H 87 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6232 (mm-30) REVERT: I 104 MET cc_start: 0.6068 (ttt) cc_final: 0.5754 (ttm) REVERT: J 74 GLN cc_start: 0.7169 (tp40) cc_final: 0.6856 (tt0) REVERT: J 81 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7346 (tt0) REVERT: J 109 LEU cc_start: 0.5945 (mm) cc_final: 0.5664 (mt) REVERT: J 119 LYS cc_start: 0.6465 (tptp) cc_final: 0.6196 (ttpt) REVERT: J 141 GLU cc_start: 0.5137 (mp0) cc_final: 0.4903 (mt-10) REVERT: K 104 MET cc_start: 0.5628 (mmp) cc_final: 0.5127 (mtp) REVERT: K 106 ARG cc_start: 0.4819 (mmp80) cc_final: 0.3355 (ttm-80) REVERT: L 106 LYS cc_start: 0.6481 (ptpt) cc_final: 0.5912 (mmtp) REVERT: L 141 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4141 (tm-30) outliers start: 75 outliers final: 53 residues processed: 352 average time/residue: 0.1915 time to fit residues: 103.2050 Evaluate side-chains 342 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 281 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 370 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 346 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 366 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.125815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103411 restraints weight = 47490.100| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.53 r_work: 0.3141 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30068 Z= 0.202 Angle : 0.605 9.974 40740 Z= 0.307 Chirality : 0.046 0.289 4567 Planarity : 0.005 0.047 5329 Dihedral : 5.431 86.108 4223 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.53 % Allowed : 15.96 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.14), residues: 3761 helix: 1.33 (0.13), residues: 1548 sheet: -0.69 (0.23), residues: 526 loop : -0.66 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 460 TYR 0.016 0.002 TYR C 428 PHE 0.017 0.002 PHE H 81 TRP 0.015 0.002 TRP A 119 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00491 (30067) covalent geometry : angle 0.60460 (40740) hydrogen bonds : bond 0.05346 ( 1291) hydrogen bonds : angle 4.67998 ( 3705) Misc. bond : bond 0.00054 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 286 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4604 (mtt) cc_final: 0.4102 (ptm) REVERT: A 54 ASP cc_start: 0.8195 (t0) cc_final: 0.7893 (t70) REVERT: A 97 LYS cc_start: 0.7032 (mtpt) cc_final: 0.6209 (mmtm) REVERT: A 98 THR cc_start: 0.7954 (m) cc_final: 0.7551 (p) REVERT: A 241 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7855 (mp) REVERT: A 257 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6295 (mt-10) REVERT: A 555 SER cc_start: 0.7433 (OUTLIER) cc_final: 0.6925 (p) REVERT: A 568 LYS cc_start: 0.7172 (mtmt) cc_final: 0.6838 (tttt) REVERT: B 156 ARG cc_start: 0.7087 (ptm160) cc_final: 0.6827 (ttp-110) REVERT: B 338 SER cc_start: 0.8937 (t) cc_final: 0.8434 (m) REVERT: B 408 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7974 (ttp80) REVERT: B 410 ASP cc_start: 0.7515 (t0) cc_final: 0.7289 (t0) REVERT: B 449 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7955 (mt-10) REVERT: B 469 GLN cc_start: 0.7758 (mt0) cc_final: 0.7373 (pp30) REVERT: B 481 ARG cc_start: 0.7944 (ttt90) cc_final: 0.7686 (ttp80) REVERT: B 482 LEU cc_start: 0.8184 (tp) cc_final: 0.7919 (tt) REVERT: B 547 ARG cc_start: 0.8241 (tpp-160) cc_final: 0.7943 (tpp-160) REVERT: B 558 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5673 (tp30) REVERT: C 130 ARG cc_start: 0.7113 (mtt90) cc_final: 0.6707 (ttm-80) REVERT: C 271 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6921 (tp30) REVERT: C 524 LYS cc_start: 0.8184 (tttm) cc_final: 0.7923 (ttmt) REVERT: D 206 GLN cc_start: 0.7504 (mt0) cc_final: 0.7274 (tm-30) REVERT: D 368 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6911 (ptmt) REVERT: E 41 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.7286 (mtp-110) REVERT: F 6 LYS cc_start: 0.7957 (tttt) cc_final: 0.7600 (tttp) REVERT: G 148 LYS cc_start: 0.7581 (mttp) cc_final: 0.7191 (mmtm) REVERT: H 1 MET cc_start: 0.5951 (tpp) cc_final: 0.5642 (tpp) REVERT: H 14 ARG cc_start: 0.6031 (mtm110) cc_final: 0.5271 (mmm-85) REVERT: H 34 GLU cc_start: 0.5605 (mt-10) cc_final: 0.5211 (mm-30) REVERT: H 87 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6262 (mm-30) REVERT: J 74 GLN cc_start: 0.7232 (tp40) cc_final: 0.6880 (tt0) REVERT: J 81 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7390 (tt0) REVERT: J 109 LEU cc_start: 0.5961 (mm) cc_final: 0.5665 (mt) REVERT: J 141 GLU cc_start: 0.5279 (mp0) cc_final: 0.5007 (mt-10) REVERT: K 104 MET cc_start: 0.5692 (mmp) cc_final: 0.5185 (mtp) REVERT: K 106 ARG cc_start: 0.5043 (mmp80) cc_final: 0.3477 (ttm-80) REVERT: L 106 LYS cc_start: 0.6508 (ptpt) cc_final: 0.5920 (mmtp) REVERT: L 141 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.4172 (tm-30) outliers start: 78 outliers final: 56 residues processed: 347 average time/residue: 0.1993 time to fit residues: 106.6336 Evaluate side-chains 343 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 280 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 252 optimal weight: 6.9990 chunk 328 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 0.0970 chunk 138 optimal weight: 10.0000 chunk 322 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 chunk 2 optimal weight: 0.0170 chunk 185 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106521 restraints weight = 47297.079| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.51 r_work: 0.3194 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30068 Z= 0.103 Angle : 0.509 10.731 40740 Z= 0.257 Chirality : 0.042 0.283 4567 Planarity : 0.004 0.045 5329 Dihedral : 4.967 85.974 4223 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.78 % Allowed : 16.81 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.14), residues: 3761 helix: 1.77 (0.14), residues: 1531 sheet: -0.60 (0.23), residues: 530 loop : -0.35 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 41 TYR 0.009 0.001 TYR C 428 PHE 0.019 0.001 PHE H 81 TRP 0.019 0.001 TRP A 119 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00223 (30067) covalent geometry : angle 0.50884 (40740) hydrogen bonds : bond 0.04091 ( 1291) hydrogen bonds : angle 4.40191 ( 3705) Misc. bond : bond 0.00012 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6176.62 seconds wall clock time: 106 minutes 12.10 seconds (6372.10 seconds total)