Starting phenix.real_space_refine on Fri Mar 6 08:12:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vas_31861/03_2026/7vas_31861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vas_31861/03_2026/7vas_31861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vas_31861/03_2026/7vas_31861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vas_31861/03_2026/7vas_31861.map" model { file = "/net/cci-nas-00/data/ceres_data/7vas_31861/03_2026/7vas_31861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vas_31861/03_2026/7vas_31861.cif" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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: 5.82, per 1000 atoms: 0.20 Number of scatterers: 29513 At special positions: 0 Unit cell: (139.04, 178.64, 151.36, 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 141 helices and 27 sheets defined 47.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 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: 3.663A 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: 4.266A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.069A 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: 3.536A 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 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.026A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.736A 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 541 removed outlier: 3.750A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.995A 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 558 through 578 removed outlier: 3.527A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (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 removed outlier: 3.511A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.958A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.751A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.600A 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 removed outlier: 3.543A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.532A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 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 543 through 550 Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 558 through 573 Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.515A pdb=" N ILE C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.920A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.416A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.050A 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 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.583A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.148A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (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: 3.749A 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: 4.116A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 4.220A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.500A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.736A pdb=" N SER D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.821A 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: 3.725A 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 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.831A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.246A 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 445 removed outlier: 3.895A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.757A 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: 3.549A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.919A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 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 231 Processing helix chain 'E' and resid 232 through 250 removed outlier: 4.534A pdb=" N ARG E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.775A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.650A 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 331 removed outlier: 3.511A pdb=" N TYR E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.776A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.971A 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: 3.911A pdb=" N LYS E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.595A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.847A 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 Processing helix chain 'F' and resid 174 through 179 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 229 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.995A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.689A 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 Processing helix chain 'F' and resid 374 through 399 Processing helix chain 'F' and resid 400 through 404 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 471 removed outlier: 3.673A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.517A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.717A pdb=" N VAL G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.635A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.707A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.798A 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: 3.541A pdb=" N ALA H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) removed outlier: 3.819A 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: 3.773A 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: 3.751A pdb=" N GLU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.594A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 99 through 115 removed outlier: 4.062A 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 134 through 137 Processing helix chain 'J' and resid 170 through 187 removed outlier: 4.693A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 3.875A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA K 110 " --> pdb=" O ARG K 106 " (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 127 through 139 removed outlier: 4.902A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.743A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.546A 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: 6.538A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.218A 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: 6.597A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.683A 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: 5.936A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.874A 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: 5.688A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.573A 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: 5.765A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.886A 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 42 through 51 removed outlier: 5.896A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.095A 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: 5.816A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 3.717A 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 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 166 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: 3.701A pdb=" N GLU A 140 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.779A 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: 6.953A 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 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 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: 6.630A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.974A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 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=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 148 removed outlier: 3.792A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.973A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.052A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 124 through 125 removed outlier: 4.791A pdb=" N VAL D 300 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.661A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 94 removed outlier: 6.851A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.621A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.562A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.709A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE F 313 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU F 257 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.663A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 278 through 280 removed outlier: 6.408A pdb=" N TYR F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 96 removed outlier: 3.518A pdb=" N GLU G 92 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.278A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU H 72 " --> pdb=" O VAL H 45 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 140 through 143 removed outlier: 3.822A pdb=" N VAL J 140 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY J 156 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU J 121 " --> pdb=" O ALA J 154 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA J 154 " --> pdb=" O LEU J 121 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3687 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: 5.38 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9671 1.34 - 1.45: 3161 1.45 - 1.57: 17032 1.57 - 1.69: 9 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 1.386 0.104 2.00e-02 2.50e+03 2.72e+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=" O1B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.589 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" N LEU H 44 " pdb=" CA LEU H 44 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.70e+00 bond pdb=" N THR B 46 " pdb=" CA THR B 46 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.59e+00 ... (remaining 30062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 40621 3.25 - 6.50: 109 6.50 - 9.76: 8 9.76 - 13.01: 1 13.01 - 16.26: 1 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 120.50 136.76 -16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" N GLY E 369 " pdb=" CA GLY E 369 " pdb=" C GLY E 369 " ideal model delta sigma weight residual 115.36 108.76 6.60 1.33e+00 5.65e-01 2.46e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O2B ADP A 601 " ideal model delta sigma weight residual 119.90 107.15 12.75 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CA GLY F 426 " pdb=" C GLY F 426 " pdb=" O GLY F 426 " ideal model delta sigma weight residual 121.41 117.77 3.64 8.80e-01 1.29e+00 1.71e+01 angle pdb=" CA ASP B 43 " pdb=" C ASP B 43 " pdb=" O ASP B 43 " ideal model delta sigma weight residual 121.49 117.10 4.39 1.16e+00 7.43e-01 1.43e+01 ... (remaining 40735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 17863 31.48 - 62.96: 432 62.96 - 94.44: 45 94.44 - 125.93: 1 125.93 - 157.41: 1 Dihedral angle restraints: 18342 sinusoidal: 7524 harmonic: 10818 Sorted by residual: dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 97.40 -157.41 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 54.01 -114.01 1 2.00e+01 2.50e-03 3.38e+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 -151.30 -28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 18339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4135 0.076 - 0.153: 424 0.153 - 0.229: 7 0.229 - 0.306: 0 0.306 - 0.382: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA THR E 371 " pdb=" N THR E 371 " pdb=" C THR E 371 " pdb=" CB THR E 371 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA LYS E 370 " pdb=" N LYS E 370 " pdb=" C LYS E 370 " pdb=" CB LYS E 370 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LEU H 44 " pdb=" N LEU H 44 " pdb=" C LEU H 44 " pdb=" CB LEU H 44 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 4564 not shown) Planarity restraints: 5329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 202 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C SER E 202 " 0.032 2.00e-02 2.50e+03 pdb=" O SER E 202 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR E 203 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 394 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 269 " -0.012 2.00e-02 2.50e+03 1.23e-02 2.64e+00 pdb=" CG PHE A 269 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 269 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 269 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 269 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 269 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 269 " -0.001 2.00e-02 2.50e+03 ... (remaining 5326 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 160 2.58 - 3.16: 23871 3.16 - 3.74: 44997 3.74 - 4.32: 62619 4.32 - 4.90: 107492 Nonbonded interactions: 239139 Sorted by model distance: nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 2.006 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 2.026 2.170 nonbonded pdb=" CD2 LEU H 44 " pdb=" CG1 VAL H 70 " model vdw 2.038 3.880 nonbonded pdb=" O PRO A 386 " pdb=" OH TYR F 331 " model vdw 2.117 3.040 nonbonded pdb=" OG SER D 431 " pdb=" OE1 GLU D 433 " model vdw 2.176 3.040 ... (remaining 239134 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 24.670 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.003 0.104 30068 Z= 0.159 Angle : 0.525 16.260 40740 Z= 0.275 Chirality : 0.043 0.382 4567 Planarity : 0.004 0.041 5329 Dihedral : 13.727 157.407 11426 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.13 % Allowed : 0.23 % Favored : 99.64 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: 1.38 (0.14), residues: 3761 helix: 2.08 (0.14), residues: 1543 sheet: 0.17 (0.22), residues: 580 loop : 0.15 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 153 TYR 0.010 0.001 TYR D 463 PHE 0.028 0.001 PHE A 269 TRP 0.010 0.001 TRP A 119 HIS 0.003 0.001 HIS J 130 Details of bonding type rmsd covalent geometry : bond 0.00334 (30067) covalent geometry : angle 0.52512 (40740) hydrogen bonds : bond 0.14777 ( 1284) hydrogen bonds : angle 5.63631 ( 3687) Misc. bond : bond 0.00024 ( 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 562 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 558 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8545 (mmm) cc_final: 0.8193 (mmm) REVERT: A 123 VAL cc_start: 0.8066 (m) cc_final: 0.7823 (p) REVERT: A 124 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7156 (mtmm) REVERT: A 156 ARG cc_start: 0.6418 (ttp80) cc_final: 0.5563 (ttt180) REVERT: A 176 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6700 (mp0) REVERT: A 264 ASP cc_start: 0.7060 (m-30) cc_final: 0.6631 (m-30) REVERT: A 456 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6768 (mp0) REVERT: A 491 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6943 (mtt-85) REVERT: B 45 ASP cc_start: 0.7353 (t0) cc_final: 0.7067 (t0) REVERT: B 48 PHE cc_start: 0.8329 (m-80) cc_final: 0.8054 (m-80) REVERT: B 130 ARG cc_start: 0.6884 (ptp-110) cc_final: 0.6653 (pmm-80) REVERT: B 161 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7869 (mptt) REVERT: B 274 ASP cc_start: 0.7978 (t70) cc_final: 0.7743 (t70) REVERT: B 326 SER cc_start: 0.8370 (m) cc_final: 0.8053 (p) REVERT: B 480 GLU cc_start: 0.7084 (mp0) cc_final: 0.6696 (mp0) REVERT: B 500 TYR cc_start: 0.8142 (m-80) cc_final: 0.7890 (m-10) REVERT: B 524 LYS cc_start: 0.8494 (ttpp) cc_final: 0.7870 (mmtp) REVERT: B 538 GLU cc_start: 0.7276 (tt0) cc_final: 0.6461 (tp30) REVERT: B 540 LEU cc_start: 0.7146 (mm) cc_final: 0.6800 (mm) REVERT: B 547 ARG cc_start: 0.7436 (mmm-85) cc_final: 0.6657 (tpp-160) REVERT: C 393 GLU cc_start: 0.7253 (tt0) cc_final: 0.7041 (tt0) REVERT: C 470 LEU cc_start: 0.7610 (mm) cc_final: 0.7256 (mt) REVERT: C 478 ASP cc_start: 0.6440 (m-30) cc_final: 0.5662 (t0) REVERT: C 481 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7482 (mmm160) REVERT: C 537 ASP cc_start: 0.6536 (m-30) cc_final: 0.6047 (m-30) REVERT: D 77 GLU cc_start: 0.7780 (tt0) cc_final: 0.7347 (tt0) REVERT: D 128 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6618 (mt-10) REVERT: D 466 LYS cc_start: 0.7251 (tttp) cc_final: 0.6895 (mmtp) REVERT: E 6 LYS cc_start: 0.7772 (tttp) cc_final: 0.7021 (ptpt) REVERT: E 25 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7907 (mtmm) REVERT: E 67 ASP cc_start: 0.8168 (p0) cc_final: 0.7787 (p0) REVERT: E 196 ILE cc_start: 0.8110 (pt) cc_final: 0.7907 (tt) REVERT: E 216 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7323 (ttm110) REVERT: E 401 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6689 (mp0) REVERT: E 420 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7174 (mmm-85) REVERT: E 428 GLN cc_start: 0.8698 (mt0) cc_final: 0.8408 (mt0) REVERT: F 6 LYS cc_start: 0.8057 (tttt) cc_final: 0.7322 (ptpt) REVERT: F 7 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7355 (mt-10) REVERT: F 380 ASP cc_start: 0.7579 (m-30) cc_final: 0.7248 (m-30) REVERT: F 450 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7364 (mm-30) REVERT: G 19 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7278 (ttt180) REVERT: G 48 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6679 (mt-10) REVERT: G 101 VAL cc_start: 0.7155 (p) cc_final: 0.6862 (p) REVERT: G 104 LEU cc_start: 0.6185 (mm) cc_final: 0.5968 (mt) REVERT: G 105 LYS cc_start: 0.4766 (tptp) cc_final: 0.3697 (ptmm) REVERT: G 146 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6639 (ttp-170) REVERT: G 149 LYS cc_start: 0.7652 (mmtt) cc_final: 0.6940 (tptt) REVERT: G 153 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6879 (mm-30) REVERT: G 202 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6390 (tm-30) REVERT: H 56 GLU cc_start: 0.6773 (pt0) cc_final: 0.6032 (pm20) REVERT: H 60 GLU cc_start: 0.6993 (tt0) cc_final: 0.6178 (pp20) REVERT: J 74 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6919 (mm-40) REVERT: J 76 ARG cc_start: 0.6315 (mtp85) cc_final: 0.5394 (mtt-85) REVERT: J 110 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6342 (tp30) REVERT: J 162 GLN cc_start: 0.7861 (mt0) cc_final: 0.7145 (mp10) REVERT: J 179 SER cc_start: 0.8148 (t) cc_final: 0.7763 (m) REVERT: K 100 ARG cc_start: 0.6049 (ttm110) cc_final: 0.5273 (mtt180) REVERT: L 76 ARG cc_start: 0.6575 (mtp-110) cc_final: 0.6294 (mtm-85) REVERT: L 81 GLU cc_start: 0.6953 (tp30) cc_final: 0.6341 (mm-30) REVERT: L 84 ARG cc_start: 0.6128 (tpt-90) cc_final: 0.5354 (tmm160) REVERT: L 85 ARG cc_start: 0.6784 (ttp80) cc_final: 0.6033 (ttp-110) REVERT: L 86 ARG cc_start: 0.7104 (mtp85) cc_final: 0.6754 (mtm-85) REVERT: L 105 ARG cc_start: 0.6423 (mtm180) cc_final: 0.6205 (mtm-85) REVERT: L 138 ARG cc_start: 0.6511 (mmm160) cc_final: 0.6268 (ttm110) REVERT: L 141 GLU cc_start: 0.6002 (tt0) cc_final: 0.5786 (tp30) REVERT: L 149 ARG cc_start: 0.7127 (ttm110) cc_final: 0.6188 (mtm110) outliers start: 4 outliers final: 2 residues processed: 562 average time/residue: 0.9626 time to fit residues: 605.9474 Evaluate side-chains 309 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain H residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 C 459 GLN D 363 ASN D 448 GLN E 166 GLN E 170 GLN E 206 GLN E 413 GLN F 170 GLN F 425 GLN F 437 GLN G 181 GLN J 165 ASN L 130 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091349 restraints weight = 44243.300| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.68 r_work: 0.2951 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30068 Z= 0.248 Angle : 0.643 7.590 40740 Z= 0.333 Chirality : 0.048 0.189 4567 Planarity : 0.006 0.060 5329 Dihedral : 6.218 154.569 4226 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.40 % Allowed : 9.57 % Favored : 88.03 % 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 are not related in a simple way. whole: 0.85 (0.14), residues: 3761 helix: 1.59 (0.13), residues: 1549 sheet: -0.03 (0.22), residues: 551 loop : -0.12 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 154 TYR 0.021 0.002 TYR F 331 PHE 0.033 0.002 PHE A 269 TRP 0.015 0.002 TRP B 119 HIS 0.007 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00613 (30067) covalent geometry : angle 0.64274 (40740) hydrogen bonds : bond 0.06430 ( 1284) hydrogen bonds : angle 4.75572 ( 3687) Misc. bond : bond 0.00240 ( 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 376 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 302 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9184 (tttt) REVERT: A 124 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7552 (mttt) REVERT: A 176 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6788 (mp0) REVERT: B 45 ASP cc_start: 0.7657 (t0) cc_final: 0.7398 (t70) REVERT: B 62 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: B 130 ARG cc_start: 0.7614 (ptp-110) cc_final: 0.7413 (ptt-90) REVERT: B 207 THR cc_start: 0.8791 (m) cc_final: 0.8589 (p) REVERT: B 524 LYS cc_start: 0.8870 (ttpp) cc_final: 0.8322 (mmtp) REVERT: B 538 GLU cc_start: 0.7508 (tt0) cc_final: 0.6600 (tp30) REVERT: B 547 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7684 (tpp-160) REVERT: C 481 ARG cc_start: 0.8391 (mtp180) cc_final: 0.8077 (mmm160) REVERT: D 77 GLU cc_start: 0.8209 (tt0) cc_final: 0.7896 (tt0) REVERT: D 373 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: D 466 LYS cc_start: 0.7629 (tttp) cc_final: 0.6935 (mmtp) REVERT: E 6 LYS cc_start: 0.8008 (tttp) cc_final: 0.7488 (ptpt) REVERT: E 25 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8297 (mttm) REVERT: E 67 ASP cc_start: 0.8600 (p0) cc_final: 0.8291 (p0) REVERT: E 274 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7302 (mtp180) REVERT: E 401 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7043 (mp0) REVERT: E 420 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7992 (mmm-85) REVERT: E 428 GLN cc_start: 0.8870 (mt0) cc_final: 0.8641 (mt0) REVERT: F 6 LYS cc_start: 0.8387 (tttt) cc_final: 0.7781 (ptpt) REVERT: F 7 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7945 (mt-10) REVERT: F 380 ASP cc_start: 0.8449 (m-30) cc_final: 0.8217 (m-30) REVERT: F 409 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7559 (mtm180) REVERT: F 450 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7882 (mm-30) REVERT: G 48 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7236 (mt-10) REVERT: G 105 LYS cc_start: 0.4936 (tptp) cc_final: 0.3808 (ptmm) REVERT: G 146 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7449 (ttp-110) REVERT: G 149 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7986 (mmmt) REVERT: G 153 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7886 (mm-30) REVERT: G 202 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6812 (tm-30) REVERT: H 56 GLU cc_start: 0.6866 (pt0) cc_final: 0.5991 (pm20) REVERT: J 110 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6344 (tp30) REVERT: J 150 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5476 (mp) REVERT: J 162 GLN cc_start: 0.8189 (mt0) cc_final: 0.7738 (mp10) REVERT: K 100 ARG cc_start: 0.6233 (ttm110) cc_final: 0.5434 (mtt180) REVERT: L 81 GLU cc_start: 0.7104 (tp30) cc_final: 0.6479 (mm-30) REVERT: L 82 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6019 (tm-30) REVERT: L 85 ARG cc_start: 0.6973 (ttp80) cc_final: 0.5816 (ttm170) REVERT: L 105 ARG cc_start: 0.6826 (mtm180) cc_final: 0.6611 (mtm-85) REVERT: L 138 ARG cc_start: 0.6529 (mmm160) cc_final: 0.6289 (mtt-85) REVERT: L 160 LYS cc_start: 0.7941 (mttm) cc_final: 0.7646 (mmtt) outliers start: 74 outliers final: 24 residues processed: 350 average time/residue: 0.8960 time to fit residues: 355.4553 Evaluate side-chains 297 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain G residue 177 ARG Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 199 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN D 448 GLN F 425 GLN L 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.093153 restraints weight = 44014.768| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.67 r_work: 0.2990 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30068 Z= 0.151 Angle : 0.540 7.199 40740 Z= 0.278 Chirality : 0.044 0.185 4567 Planarity : 0.005 0.046 5329 Dihedral : 5.969 149.911 4224 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.14 % Allowed : 12.59 % Favored : 85.27 % 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 are not related in a simple way. whole: 0.99 (0.14), residues: 3761 helix: 1.79 (0.13), residues: 1549 sheet: -0.06 (0.22), residues: 560 loop : -0.10 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 345 TYR 0.013 0.001 TYR H 42 PHE 0.020 0.002 PHE A 269 TRP 0.014 0.001 TRP B 119 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00358 (30067) covalent geometry : angle 0.54009 (40740) hydrogen bonds : bond 0.05277 ( 1284) hydrogen bonds : angle 4.48444 ( 3687) Misc. bond : bond 0.00109 ( 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 353 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 287 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7945 (mmm160) REVERT: A 124 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7552 (mttt) REVERT: A 524 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7739 (mptt) REVERT: B 62 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: B 524 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8366 (mmtp) REVERT: B 527 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: B 538 GLU cc_start: 0.7510 (tt0) cc_final: 0.6527 (tp30) REVERT: B 540 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7166 (mm) REVERT: B 547 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7553 (tpp-160) REVERT: C 316 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8753 (tt0) REVERT: C 470 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7340 (mt) REVERT: D 77 GLU cc_start: 0.8183 (tt0) cc_final: 0.7885 (tt0) REVERT: D 445 MET cc_start: 0.8659 (mtt) cc_final: 0.8384 (mtt) REVERT: D 466 LYS cc_start: 0.7717 (tttp) cc_final: 0.6923 (mmtp) REVERT: E 6 LYS cc_start: 0.7993 (tttp) cc_final: 0.7473 (ptpt) REVERT: E 67 ASP cc_start: 0.8605 (p0) cc_final: 0.8303 (p0) REVERT: E 274 ARG cc_start: 0.7778 (mmm160) cc_final: 0.7236 (mtp180) REVERT: E 401 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7045 (mp0) REVERT: E 420 ARG cc_start: 0.8256 (mmm160) cc_final: 0.8003 (mmm-85) REVERT: E 428 GLN cc_start: 0.8856 (mt0) cc_final: 0.8620 (mt0) REVERT: F 6 LYS cc_start: 0.8398 (tttt) cc_final: 0.7834 (ptpt) REVERT: F 7 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7835 (mt-10) REVERT: F 248 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: F 380 ASP cc_start: 0.8393 (m-30) cc_final: 0.8127 (m-30) REVERT: F 409 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7565 (mtm180) REVERT: F 450 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7832 (mm-30) REVERT: G 105 LYS cc_start: 0.4877 (tptp) cc_final: 0.3758 (ptmm) REVERT: G 124 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6016 (tm) REVERT: G 146 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7478 (ttp-170) REVERT: G 149 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8091 (mmmt) REVERT: G 153 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7855 (mm-30) REVERT: G 202 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6755 (tm-30) REVERT: H 38 GLU cc_start: 0.5965 (mt-10) cc_final: 0.5563 (pp20) REVERT: H 78 LYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5951 (pttm) REVERT: H 89 TYR cc_start: 0.7498 (t80) cc_final: 0.7294 (t80) REVERT: J 89 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6130 (mp0) REVERT: J 110 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6321 (tp30) REVERT: J 113 GLU cc_start: 0.7190 (tt0) cc_final: 0.6945 (tt0) REVERT: J 122 VAL cc_start: 0.4861 (OUTLIER) cc_final: 0.4617 (p) REVERT: J 150 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5225 (mp) REVERT: J 162 GLN cc_start: 0.8221 (mt0) cc_final: 0.7783 (mp10) REVERT: K 100 ARG cc_start: 0.6229 (ttm110) cc_final: 0.5410 (mtt180) REVERT: K 101 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7145 (mm-30) REVERT: L 81 GLU cc_start: 0.7126 (tp30) cc_final: 0.6513 (mm-30) REVERT: L 82 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.5967 (tm-30) REVERT: L 85 ARG cc_start: 0.6952 (ttp80) cc_final: 0.5829 (ttm170) REVERT: L 105 ARG cc_start: 0.6900 (mtm180) cc_final: 0.6674 (mtm-85) REVERT: L 138 ARG cc_start: 0.6569 (mmm160) cc_final: 0.6279 (mtt-85) outliers start: 66 outliers final: 24 residues processed: 332 average time/residue: 0.8909 time to fit residues: 335.8830 Evaluate side-chains 298 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 409 ARG Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 279 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN C 459 GLN D 170 GLN D 448 GLN E 465 GLN F 425 GLN L 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.090993 restraints weight = 43895.309| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.67 r_work: 0.2955 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30068 Z= 0.235 Angle : 0.617 7.322 40740 Z= 0.319 Chirality : 0.047 0.186 4567 Planarity : 0.005 0.048 5329 Dihedral : 6.173 143.250 4224 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.66 % Allowed : 14.37 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3761 helix: 1.52 (0.13), residues: 1546 sheet: -0.27 (0.22), residues: 574 loop : -0.28 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 130 TYR 0.017 0.002 TYR F 331 PHE 0.025 0.002 PHE A 269 TRP 0.014 0.002 TRP L 100 HIS 0.005 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00578 (30067) covalent geometry : angle 0.61723 (40740) hydrogen bonds : bond 0.06145 ( 1284) hydrogen bonds : angle 4.59497 ( 3687) Misc. bond : bond 0.00165 ( 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 353 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 271 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9164 (tttt) REVERT: A 83 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 93 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7859 (mmm160) REVERT: A 124 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7505 (mttt) REVERT: A 209 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7924 (mtm) REVERT: B 62 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: B 524 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8356 (mmtp) REVERT: B 527 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: B 538 GLU cc_start: 0.7617 (tt0) cc_final: 0.6620 (tp30) REVERT: B 540 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7099 (mm) REVERT: B 547 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7259 (tpp-160) REVERT: C 316 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8845 (tp40) REVERT: C 470 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7288 (mt) REVERT: C 538 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: D 43 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7890 (ptt180) REVERT: D 77 GLU cc_start: 0.8192 (tt0) cc_final: 0.7895 (tt0) REVERT: D 445 MET cc_start: 0.8691 (mtm) cc_final: 0.8414 (mtt) REVERT: D 466 LYS cc_start: 0.7788 (tttp) cc_final: 0.6872 (mmtp) REVERT: E 6 LYS cc_start: 0.8005 (tttp) cc_final: 0.7526 (ptpt) REVERT: E 67 ASP cc_start: 0.8672 (p0) cc_final: 0.8373 (p0) REVERT: E 274 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7274 (mtp180) REVERT: E 302 GLU cc_start: 0.8245 (pp20) cc_final: 0.7978 (pt0) REVERT: E 401 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7039 (mp0) REVERT: E 404 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8359 (mp) REVERT: E 420 ARG cc_start: 0.8337 (mmm160) cc_final: 0.8044 (mmm-85) REVERT: E 428 GLN cc_start: 0.8828 (mt0) cc_final: 0.8594 (mt0) REVERT: F 6 LYS cc_start: 0.8398 (tttt) cc_final: 0.7821 (ptpt) REVERT: F 7 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7902 (mt-10) REVERT: F 248 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: F 380 ASP cc_start: 0.8481 (m-30) cc_final: 0.8267 (m-30) REVERT: F 450 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7842 (mm-30) REVERT: G 105 LYS cc_start: 0.4800 (tptp) cc_final: 0.3793 (ptmm) REVERT: G 124 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6035 (tm) REVERT: G 146 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7474 (ttp-170) REVERT: G 149 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8071 (mmmt) REVERT: G 153 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7814 (mm-30) REVERT: G 202 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6756 (tm-30) REVERT: H 15 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7374 (tp) REVERT: H 38 GLU cc_start: 0.5801 (mt-10) cc_final: 0.5455 (pp20) REVERT: J 110 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6293 (tp30) REVERT: J 122 VAL cc_start: 0.4611 (OUTLIER) cc_final: 0.4301 (p) REVERT: J 150 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5269 (mp) REVERT: J 162 GLN cc_start: 0.8262 (mt0) cc_final: 0.7794 (mp10) REVERT: J 172 ASP cc_start: 0.7206 (m-30) cc_final: 0.6771 (t70) REVERT: K 100 ARG cc_start: 0.6231 (ttm110) cc_final: 0.5396 (mtt180) REVERT: L 81 GLU cc_start: 0.7052 (tp30) cc_final: 0.6437 (mm-30) REVERT: L 82 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6029 (tm-30) REVERT: L 85 ARG cc_start: 0.6910 (ttp80) cc_final: 0.5760 (ttm170) REVERT: L 105 ARG cc_start: 0.6846 (mtm180) cc_final: 0.6631 (mtm-85) REVERT: L 138 ARG cc_start: 0.6743 (mmm160) cc_final: 0.6233 (mmm160) outliers start: 82 outliers final: 31 residues processed: 327 average time/residue: 0.8782 time to fit residues: 327.2011 Evaluate side-chains 305 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 15 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 354 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 322 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 278 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN D 448 GLN F 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.091843 restraints weight = 43956.968| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.74 r_work: 0.2960 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30068 Z= 0.167 Angle : 0.552 7.190 40740 Z= 0.284 Chirality : 0.044 0.203 4567 Planarity : 0.005 0.047 5329 Dihedral : 6.016 138.377 4224 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.37 % Allowed : 15.35 % Favored : 82.28 % 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 are not related in a simple way. whole: 0.74 (0.14), residues: 3761 helix: 1.64 (0.13), residues: 1550 sheet: -0.29 (0.22), residues: 580 loop : -0.25 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 130 TYR 0.011 0.001 TYR C 25 PHE 0.017 0.002 PHE B 143 TRP 0.014 0.001 TRP L 100 HIS 0.007 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00401 (30067) covalent geometry : angle 0.55228 (40740) hydrogen bonds : bond 0.05433 ( 1284) hydrogen bonds : angle 4.46249 ( 3687) Misc. bond : bond 0.00089 ( 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 350 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 277 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9164 (tttt) REVERT: A 93 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7882 (mmm160) REVERT: A 124 LYS cc_start: 0.8018 (mtmm) cc_final: 0.7565 (mttt) REVERT: A 524 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7826 (mptt) REVERT: B 45 ASP cc_start: 0.7605 (t0) cc_final: 0.7277 (t70) REVERT: B 62 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: B 158 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7329 (ttmm) REVERT: B 269 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 524 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8393 (mmtp) REVERT: B 527 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: B 538 GLU cc_start: 0.7605 (tt0) cc_final: 0.6601 (tp30) REVERT: B 540 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7160 (mm) REVERT: B 547 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7349 (tpp-160) REVERT: C 316 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8816 (tt0) REVERT: C 470 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7305 (mt) REVERT: C 538 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: D 43 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7905 (ptt180) REVERT: D 77 GLU cc_start: 0.8174 (tt0) cc_final: 0.7901 (mt-10) REVERT: D 466 LYS cc_start: 0.7758 (tttp) cc_final: 0.6913 (mmtp) REVERT: E 6 LYS cc_start: 0.8021 (tttp) cc_final: 0.7569 (ptpt) REVERT: E 67 ASP cc_start: 0.8703 (p0) cc_final: 0.8414 (p0) REVERT: E 274 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7312 (mtp180) REVERT: E 302 GLU cc_start: 0.8202 (pp20) cc_final: 0.7957 (pt0) REVERT: E 401 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7102 (mp0) REVERT: E 404 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8358 (mp) REVERT: E 420 ARG cc_start: 0.8339 (mmm160) cc_final: 0.8067 (mmm-85) REVERT: E 428 GLN cc_start: 0.8844 (mt0) cc_final: 0.8614 (mt0) REVERT: F 6 LYS cc_start: 0.8375 (tttt) cc_final: 0.7882 (ptpt) REVERT: F 7 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F 36 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8590 (ttmt) REVERT: F 248 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: F 334 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: F 380 ASP cc_start: 0.8481 (m-30) cc_final: 0.8242 (m-30) REVERT: F 425 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: F 450 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7820 (mm-30) REVERT: G 105 LYS cc_start: 0.4871 (tptp) cc_final: 0.3787 (ptmm) REVERT: G 124 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.5990 (tm) REVERT: G 146 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7516 (ttp-170) REVERT: G 149 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8098 (mmmt) REVERT: G 153 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7916 (mm-30) REVERT: G 202 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6770 (tm-30) REVERT: H 15 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7345 (tp) REVERT: H 38 GLU cc_start: 0.5798 (mt-10) cc_final: 0.5368 (pp20) REVERT: H 89 TYR cc_start: 0.7634 (t80) cc_final: 0.7368 (t80) REVERT: J 88 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7009 (ttp80) REVERT: J 110 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6342 (tp30) REVERT: J 122 VAL cc_start: 0.4627 (OUTLIER) cc_final: 0.4335 (p) REVERT: J 150 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5122 (mp) REVERT: J 162 GLN cc_start: 0.8269 (mt0) cc_final: 0.7848 (mp10) REVERT: J 172 ASP cc_start: 0.7200 (m-30) cc_final: 0.6790 (t70) REVERT: K 100 ARG cc_start: 0.6199 (ttm110) cc_final: 0.5372 (mtt180) REVERT: K 101 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7017 (mm-30) REVERT: L 81 GLU cc_start: 0.7146 (tp30) cc_final: 0.6547 (mm-30) REVERT: L 82 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: L 85 ARG cc_start: 0.6879 (ttp80) cc_final: 0.5763 (ttm170) REVERT: L 105 ARG cc_start: 0.6893 (mtm180) cc_final: 0.6687 (mtm-85) REVERT: L 138 ARG cc_start: 0.6745 (mmm160) cc_final: 0.6204 (mmm160) REVERT: L 160 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7493 (mttm) REVERT: L 161 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8134 (t) outliers start: 73 outliers final: 31 residues processed: 334 average time/residue: 0.8831 time to fit residues: 336.1360 Evaluate side-chains 315 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 260 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 161 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 355 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 357 optimal weight: 30.0000 chunk 364 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN D 448 GLN F 425 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.091770 restraints weight = 43868.827| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.74 r_work: 0.2962 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30068 Z= 0.160 Angle : 0.543 7.271 40740 Z= 0.279 Chirality : 0.044 0.210 4567 Planarity : 0.005 0.046 5329 Dihedral : 5.942 136.134 4223 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.66 % Allowed : 15.44 % Favored : 81.89 % 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 are not related in a simple way. whole: 0.80 (0.14), residues: 3761 helix: 1.71 (0.13), residues: 1561 sheet: -0.28 (0.21), residues: 594 loop : -0.23 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 130 TYR 0.010 0.001 TYR C 428 PHE 0.016 0.002 PHE C 559 TRP 0.014 0.001 TRP L 100 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00383 (30067) covalent geometry : angle 0.54340 (40740) hydrogen bonds : bond 0.05275 ( 1284) hydrogen bonds : angle 4.40769 ( 3687) Misc. bond : bond 0.00125 ( 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 355 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 273 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9175 (tttt) REVERT: A 93 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7842 (mmm160) REVERT: A 124 LYS cc_start: 0.7913 (mtmm) cc_final: 0.7456 (mttt) REVERT: A 524 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7811 (mptt) REVERT: B 45 ASP cc_start: 0.7591 (t0) cc_final: 0.7267 (t70) REVERT: B 62 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: B 158 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7317 (ttmm) REVERT: B 269 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8259 (t80) REVERT: B 524 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8360 (mmtp) REVERT: B 527 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: B 538 GLU cc_start: 0.7597 (tt0) cc_final: 0.6579 (tp30) REVERT: B 540 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7125 (mm) REVERT: B 547 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7338 (tpp-160) REVERT: C 316 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8848 (tt0) REVERT: C 470 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7285 (mt) REVERT: C 538 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: D 77 GLU cc_start: 0.8182 (tt0) cc_final: 0.7915 (mt-10) REVERT: D 466 LYS cc_start: 0.7756 (tttp) cc_final: 0.6902 (mmtp) REVERT: E 6 LYS cc_start: 0.8035 (tttp) cc_final: 0.7572 (ptpt) REVERT: E 274 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7305 (mtp180) REVERT: E 302 GLU cc_start: 0.8243 (pp20) cc_final: 0.7966 (pt0) REVERT: E 401 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7137 (mp0) REVERT: E 404 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8364 (mp) REVERT: E 420 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8049 (mmm-85) REVERT: E 428 GLN cc_start: 0.8840 (mt0) cc_final: 0.8614 (mt0) REVERT: F 6 LYS cc_start: 0.8328 (tttt) cc_final: 0.7874 (ptpt) REVERT: F 7 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7947 (mt-10) REVERT: F 36 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8578 (ttmt) REVERT: F 248 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: F 334 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: F 380 ASP cc_start: 0.8480 (m-30) cc_final: 0.8247 (m-30) REVERT: F 425 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: F 450 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7801 (mm-30) REVERT: G 105 LYS cc_start: 0.4836 (tptp) cc_final: 0.3804 (ptmm) REVERT: G 124 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6048 (tm) REVERT: G 146 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7547 (ttp-170) REVERT: G 149 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8139 (mmmt) REVERT: G 153 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7878 (mm-30) REVERT: G 202 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6740 (tm-30) REVERT: H 89 TYR cc_start: 0.7583 (t80) cc_final: 0.7322 (t80) REVERT: J 88 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6982 (ttp80) REVERT: J 96 GLN cc_start: 0.6043 (mt0) cc_final: 0.5386 (tp40) REVERT: J 110 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6340 (tp30) REVERT: J 122 VAL cc_start: 0.4416 (OUTLIER) cc_final: 0.4110 (p) REVERT: J 150 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5096 (mp) REVERT: J 162 GLN cc_start: 0.8276 (mt0) cc_final: 0.7856 (mp10) REVERT: J 172 ASP cc_start: 0.7184 (m-30) cc_final: 0.6778 (t70) REVERT: K 100 ARG cc_start: 0.6176 (ttm110) cc_final: 0.5376 (mtt180) REVERT: L 74 GLN cc_start: 0.7559 (mm-40) cc_final: 0.6976 (mm110) REVERT: L 81 GLU cc_start: 0.7142 (tp30) cc_final: 0.6609 (mm-30) REVERT: L 82 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5964 (tm-30) REVERT: L 85 ARG cc_start: 0.6863 (ttp80) cc_final: 0.5744 (ttm170) REVERT: L 105 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6659 (mtm-85) REVERT: L 138 ARG cc_start: 0.6779 (mmm160) cc_final: 0.6212 (mmm160) REVERT: L 161 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8136 (t) outliers start: 82 outliers final: 38 residues processed: 338 average time/residue: 0.8568 time to fit residues: 331.2566 Evaluate side-chains 319 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 161 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 6 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN D 448 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092041 restraints weight = 44054.400| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.68 r_work: 0.2964 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30068 Z= 0.190 Angle : 0.573 7.359 40740 Z= 0.295 Chirality : 0.045 0.218 4567 Planarity : 0.005 0.046 5329 Dihedral : 6.003 140.387 4223 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.73 % Allowed : 15.77 % 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 are not related in a simple way. whole: 0.70 (0.14), residues: 3761 helix: 1.64 (0.13), residues: 1555 sheet: -0.35 (0.21), residues: 582 loop : -0.30 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 130 TYR 0.012 0.001 TYR C 428 PHE 0.018 0.002 PHE C 559 TRP 0.014 0.002 TRP L 100 HIS 0.004 0.001 HIS F 252 Details of bonding type rmsd covalent geometry : bond 0.00464 (30067) covalent geometry : angle 0.57274 (40740) hydrogen bonds : bond 0.05553 ( 1284) hydrogen bonds : angle 4.45534 ( 3687) Misc. bond : bond 0.00115 ( 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 355 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 271 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9185 (tttt) REVERT: A 93 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7864 (mmm160) REVERT: A 124 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7481 (mttt) REVERT: A 491 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7951 (mtt-85) REVERT: A 524 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7836 (mptt) REVERT: B 45 ASP cc_start: 0.7656 (t70) cc_final: 0.7294 (t70) REVERT: B 62 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: B 158 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7356 (ttmm) REVERT: B 269 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8291 (t80) REVERT: B 524 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8387 (mmtp) REVERT: B 527 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: B 538 GLU cc_start: 0.7573 (tt0) cc_final: 0.6555 (tp30) REVERT: B 540 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7133 (mm) REVERT: B 547 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7368 (tpp-160) REVERT: C 470 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7335 (mt) REVERT: C 538 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: D 77 GLU cc_start: 0.8202 (tt0) cc_final: 0.7942 (mt-10) REVERT: D 445 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: E 6 LYS cc_start: 0.8049 (tttp) cc_final: 0.7600 (ptpt) REVERT: E 274 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7323 (mtp180) REVERT: E 302 GLU cc_start: 0.8277 (pp20) cc_final: 0.8020 (pt0) REVERT: E 401 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7137 (mp0) REVERT: E 404 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8366 (mp) REVERT: E 420 ARG cc_start: 0.8350 (mmm160) cc_final: 0.8064 (mmm-85) REVERT: E 428 GLN cc_start: 0.8829 (mt0) cc_final: 0.8606 (mt0) REVERT: F 6 LYS cc_start: 0.8325 (tttt) cc_final: 0.7873 (ptpt) REVERT: F 7 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7920 (mt-10) REVERT: F 36 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (ttmt) REVERT: F 248 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: F 334 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: F 380 ASP cc_start: 0.8478 (m-30) cc_final: 0.8241 (m-30) REVERT: G 105 LYS cc_start: 0.4939 (tptp) cc_final: 0.3926 (ptmt) REVERT: G 124 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5982 (tm) REVERT: G 146 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7517 (ttp-170) REVERT: G 149 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8190 (mmmt) REVERT: G 153 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7899 (mm-30) REVERT: G 202 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6789 (tm-30) REVERT: H 8 GLU cc_start: 0.6104 (mp0) cc_final: 0.5322 (tm-30) REVERT: H 38 GLU cc_start: 0.5844 (mt-10) cc_final: 0.5384 (pp20) REVERT: H 56 GLU cc_start: 0.6844 (pt0) cc_final: 0.5880 (pm20) REVERT: H 79 GLU cc_start: 0.6672 (tp30) cc_final: 0.6153 (tm-30) REVERT: H 89 TYR cc_start: 0.7580 (t80) cc_final: 0.7289 (t80) REVERT: J 88 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6334 (ttp80) REVERT: J 96 GLN cc_start: 0.6158 (mt0) cc_final: 0.5467 (tp-100) REVERT: J 110 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6308 (tp30) REVERT: J 122 VAL cc_start: 0.4419 (OUTLIER) cc_final: 0.4112 (p) REVERT: J 150 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5103 (mp) REVERT: J 162 GLN cc_start: 0.8261 (mt0) cc_final: 0.7861 (mp10) REVERT: J 172 ASP cc_start: 0.7253 (m-30) cc_final: 0.6908 (t70) REVERT: K 100 ARG cc_start: 0.6205 (ttm110) cc_final: 0.5577 (mtt180) REVERT: K 101 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6984 (mm-30) REVERT: L 74 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7034 (mm110) REVERT: L 81 GLU cc_start: 0.7165 (tp30) cc_final: 0.6640 (mm-30) REVERT: L 82 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6003 (tm-30) REVERT: L 85 ARG cc_start: 0.6906 (ttp80) cc_final: 0.5766 (ttm170) REVERT: L 105 ARG cc_start: 0.6899 (mtm180) cc_final: 0.6684 (mtm-85) REVERT: L 138 ARG cc_start: 0.6781 (mmm160) cc_final: 0.6292 (mmm160) REVERT: L 161 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8148 (t) outliers start: 84 outliers final: 44 residues processed: 336 average time/residue: 0.8431 time to fit residues: 323.8615 Evaluate side-chains 327 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 263 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 161 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 117 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 372 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 69 optimal weight: 0.0770 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN D 448 GLN F 425 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.091563 restraints weight = 44007.197| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.75 r_work: 0.2962 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30068 Z= 0.192 Angle : 0.573 8.353 40740 Z= 0.295 Chirality : 0.045 0.222 4567 Planarity : 0.005 0.046 5329 Dihedral : 6.032 145.775 4223 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.63 % Allowed : 16.09 % Favored : 81.28 % 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 are not related in a simple way. whole: 0.67 (0.14), residues: 3761 helix: 1.62 (0.13), residues: 1555 sheet: -0.29 (0.22), residues: 572 loop : -0.36 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 130 TYR 0.012 0.001 TYR C 428 PHE 0.018 0.002 PHE C 559 TRP 0.014 0.002 TRP L 100 HIS 0.004 0.001 HIS F 252 Details of bonding type rmsd covalent geometry : bond 0.00467 (30067) covalent geometry : angle 0.57344 (40740) hydrogen bonds : bond 0.05596 ( 1284) hydrogen bonds : angle 4.46446 ( 3687) Misc. bond : bond 0.00122 ( 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 353 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 272 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9184 (tttt) REVERT: A 93 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7894 (mmm160) REVERT: A 124 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7454 (mttt) REVERT: A 491 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7986 (mtt-85) REVERT: A 524 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7854 (mptt) REVERT: B 45 ASP cc_start: 0.7623 (t70) cc_final: 0.7285 (t70) REVERT: B 62 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: B 158 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7400 (ttmm) REVERT: B 269 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8296 (t80) REVERT: B 524 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8383 (mmtp) REVERT: B 527 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: B 538 GLU cc_start: 0.7629 (tt0) cc_final: 0.6584 (tp30) REVERT: B 540 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7116 (mm) REVERT: B 547 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7266 (tpp-160) REVERT: C 124 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8269 (tppt) REVERT: C 470 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7375 (mt) REVERT: C 538 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: D 77 GLU cc_start: 0.8210 (tt0) cc_final: 0.7924 (mt-10) REVERT: D 115 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8075 (p) REVERT: D 445 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8318 (mtt) REVERT: E 6 LYS cc_start: 0.8034 (tttp) cc_final: 0.7589 (ptpt) REVERT: E 274 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7328 (mtp180) REVERT: E 302 GLU cc_start: 0.8336 (pp20) cc_final: 0.8019 (pt0) REVERT: E 401 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7151 (mp0) REVERT: E 404 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8368 (mp) REVERT: E 420 ARG cc_start: 0.8357 (mmm160) cc_final: 0.8071 (mmm-85) REVERT: E 428 GLN cc_start: 0.8827 (mt0) cc_final: 0.8615 (mt0) REVERT: F 6 LYS cc_start: 0.8326 (tttt) cc_final: 0.7853 (ptpt) REVERT: F 7 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7955 (mt-10) REVERT: F 36 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8599 (ttmt) REVERT: F 248 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: F 334 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: F 380 ASP cc_start: 0.8479 (m-30) cc_final: 0.8240 (m-30) REVERT: G 105 LYS cc_start: 0.4974 (tptp) cc_final: 0.3932 (ptmm) REVERT: G 124 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.5889 (tm) REVERT: G 146 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7521 (ttp-170) REVERT: G 149 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8197 (mmmt) REVERT: G 153 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7933 (mm-30) REVERT: G 202 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6767 (tm-30) REVERT: H 8 GLU cc_start: 0.5979 (mp0) cc_final: 0.5192 (tm-30) REVERT: H 38 GLU cc_start: 0.5898 (mt-10) cc_final: 0.5406 (pp20) REVERT: H 56 GLU cc_start: 0.6839 (pt0) cc_final: 0.5868 (pm20) REVERT: H 78 LYS cc_start: 0.6741 (mmpt) cc_final: 0.6359 (mttp) REVERT: H 79 GLU cc_start: 0.6642 (tp30) cc_final: 0.6178 (tm-30) REVERT: H 89 TYR cc_start: 0.7513 (t80) cc_final: 0.7200 (t80) REVERT: I 93 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5934 (mp0) REVERT: J 88 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6267 (ttp80) REVERT: J 96 GLN cc_start: 0.6222 (mt0) cc_final: 0.5496 (tp-100) REVERT: J 110 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6268 (tp30) REVERT: J 122 VAL cc_start: 0.4391 (OUTLIER) cc_final: 0.4067 (p) REVERT: J 150 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.5064 (mp) REVERT: J 162 GLN cc_start: 0.8249 (mt0) cc_final: 0.7847 (mp10) REVERT: J 172 ASP cc_start: 0.7213 (m-30) cc_final: 0.6897 (t70) REVERT: K 100 ARG cc_start: 0.6166 (ttm110) cc_final: 0.5539 (mtt180) REVERT: K 101 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6974 (mm-30) REVERT: L 74 GLN cc_start: 0.7521 (mm-40) cc_final: 0.6995 (mm110) REVERT: L 81 GLU cc_start: 0.7114 (tp30) cc_final: 0.6591 (mm-30) REVERT: L 82 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6022 (tm-30) REVERT: L 85 ARG cc_start: 0.6909 (ttp80) cc_final: 0.5751 (ttm170) REVERT: L 138 ARG cc_start: 0.6783 (mmm160) cc_final: 0.6292 (mmm160) REVERT: L 161 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8126 (t) outliers start: 81 outliers final: 42 residues processed: 337 average time/residue: 0.8293 time to fit residues: 319.0120 Evaluate side-chains 333 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 269 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 161 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 62 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 280 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 356 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 316 GLN C 316 GLN D 448 GLN F 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092665 restraints weight = 43822.255| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.65 r_work: 0.2989 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30068 Z= 0.130 Angle : 0.528 7.507 40740 Z= 0.270 Chirality : 0.043 0.243 4567 Planarity : 0.004 0.055 5329 Dihedral : 5.838 144.547 4223 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.91 % Allowed : 16.90 % Favored : 81.18 % 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 are not related in a simple way. whole: 0.88 (0.14), residues: 3761 helix: 1.81 (0.13), residues: 1563 sheet: -0.18 (0.22), residues: 562 loop : -0.28 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 130 TYR 0.010 0.001 TYR G 133 PHE 0.014 0.001 PHE A 230 TRP 0.019 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00301 (30067) covalent geometry : angle 0.52756 (40740) hydrogen bonds : bond 0.04854 ( 1284) hydrogen bonds : angle 4.33966 ( 3687) Misc. bond : bond 0.00050 ( 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 332 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 273 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7846 (mmm160) REVERT: A 124 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7435 (mttt) REVERT: A 491 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7934 (mtt-85) REVERT: A 524 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7775 (mptt) REVERT: B 45 ASP cc_start: 0.7620 (t70) cc_final: 0.7326 (t70) REVERT: B 62 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: B 158 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7355 (ttmm) REVERT: B 269 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8235 (t80) REVERT: B 524 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8363 (mmtp) REVERT: B 538 GLU cc_start: 0.7582 (tt0) cc_final: 0.6564 (tp30) REVERT: B 547 ARG cc_start: 0.7751 (mmm-85) cc_final: 0.7301 (tpp-160) REVERT: C 124 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8257 (tppt) REVERT: C 470 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7403 (mt) REVERT: C 538 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: D 77 GLU cc_start: 0.8162 (tt0) cc_final: 0.7866 (mt-10) REVERT: D 115 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8068 (p) REVERT: E 6 LYS cc_start: 0.7998 (tttp) cc_final: 0.7554 (ptpt) REVERT: E 274 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7286 (mtp180) REVERT: E 302 GLU cc_start: 0.8311 (pp20) cc_final: 0.8035 (pt0) REVERT: E 401 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7135 (mp0) REVERT: E 420 ARG cc_start: 0.8314 (mmm160) cc_final: 0.8007 (mmm-85) REVERT: E 428 GLN cc_start: 0.8831 (mt0) cc_final: 0.8613 (mt0) REVERT: F 6 LYS cc_start: 0.8298 (tttt) cc_final: 0.7796 (mttt) REVERT: F 7 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7907 (mt-10) REVERT: F 36 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8574 (ttmt) REVERT: F 248 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: F 380 ASP cc_start: 0.8432 (m-30) cc_final: 0.8195 (m-30) REVERT: G 105 LYS cc_start: 0.4962 (tptp) cc_final: 0.4044 (pttp) REVERT: G 124 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5844 (tm) REVERT: G 146 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7502 (ttp-170) REVERT: G 149 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8276 (tptp) REVERT: G 153 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7908 (mm-30) REVERT: G 202 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6724 (tm-30) REVERT: H 38 GLU cc_start: 0.5915 (mt-10) cc_final: 0.5436 (pp20) REVERT: H 56 GLU cc_start: 0.6840 (pt0) cc_final: 0.5858 (pm20) REVERT: H 78 LYS cc_start: 0.6680 (mmpt) cc_final: 0.6353 (mttp) REVERT: H 79 GLU cc_start: 0.6623 (tp30) cc_final: 0.6110 (tm-30) REVERT: H 89 TYR cc_start: 0.7487 (t80) cc_final: 0.7172 (t80) REVERT: I 93 GLU cc_start: 0.6370 (mm-30) cc_final: 0.5942 (mp0) REVERT: J 88 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6172 (ttp80) REVERT: J 96 GLN cc_start: 0.6159 (mt0) cc_final: 0.5539 (tp40) REVERT: J 110 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6329 (tp30) REVERT: J 150 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.4994 (mp) REVERT: J 162 GLN cc_start: 0.8212 (mt0) cc_final: 0.7804 (mp10) REVERT: J 172 ASP cc_start: 0.7216 (m-30) cc_final: 0.6793 (t70) REVERT: K 100 ARG cc_start: 0.6220 (ttm110) cc_final: 0.5458 (mtt180) REVERT: K 101 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6963 (mm-30) REVERT: L 74 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7003 (mm110) REVERT: L 81 GLU cc_start: 0.7106 (tp30) cc_final: 0.6582 (mm-30) REVERT: L 82 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.5984 (tm-30) REVERT: L 85 ARG cc_start: 0.6930 (ttp80) cc_final: 0.5758 (ttm170) REVERT: L 138 ARG cc_start: 0.6657 (mmm160) cc_final: 0.6177 (mmm160) REVERT: L 161 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8123 (t) outliers start: 59 outliers final: 30 residues processed: 321 average time/residue: 0.8011 time to fit residues: 293.6343 Evaluate side-chains 312 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 161 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 370 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN D 448 GLN F 310 GLN F 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.090518 restraints weight = 44062.732| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.74 r_work: 0.2940 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 30068 Z= 0.269 Angle : 0.647 8.171 40740 Z= 0.335 Chirality : 0.049 0.229 4567 Planarity : 0.006 0.057 5329 Dihedral : 6.222 152.093 4223 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.98 % Allowed : 17.07 % Favored : 80.95 % 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 are not related in a simple way. whole: 0.44 (0.14), residues: 3761 helix: 1.42 (0.13), residues: 1558 sheet: -0.38 (0.22), residues: 565 loop : -0.48 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 417 TYR 0.016 0.002 TYR G 61 PHE 0.024 0.002 PHE C 559 TRP 0.020 0.002 TRP A 119 HIS 0.008 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00664 (30067) covalent geometry : angle 0.64680 (40740) hydrogen bonds : bond 0.06385 ( 1284) hydrogen bonds : angle 4.60944 ( 3687) Misc. bond : bond 0.00204 ( 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 321 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9184 (tttt) REVERT: A 93 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7909 (mmm160) REVERT: A 124 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7432 (mttt) REVERT: A 491 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7973 (mtt-85) REVERT: A 524 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7870 (mptt) REVERT: B 45 ASP cc_start: 0.7681 (t70) cc_final: 0.7331 (t70) REVERT: B 62 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: B 158 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7434 (ttmm) REVERT: B 269 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8289 (t80) REVERT: B 417 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7815 (mmm-85) REVERT: B 524 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8394 (mmtp) REVERT: B 538 GLU cc_start: 0.7542 (tt0) cc_final: 0.6515 (tp30) REVERT: B 547 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7272 (tpp-160) REVERT: C 470 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7408 (mt) REVERT: C 538 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: D 77 GLU cc_start: 0.8217 (tt0) cc_final: 0.7955 (mt-10) REVERT: D 115 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8131 (p) REVERT: E 6 LYS cc_start: 0.8016 (tttp) cc_final: 0.7601 (ptpt) REVERT: E 274 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7350 (mtp180) REVERT: E 302 GLU cc_start: 0.8472 (pp20) cc_final: 0.8067 (pt0) REVERT: E 401 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7204 (mp0) REVERT: E 420 ARG cc_start: 0.8367 (mmm160) cc_final: 0.8070 (mmm-85) REVERT: E 428 GLN cc_start: 0.8816 (mt0) cc_final: 0.8597 (mt0) REVERT: F 6 LYS cc_start: 0.8346 (tttt) cc_final: 0.7824 (ptpt) REVERT: F 7 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7993 (mt-10) REVERT: F 36 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8611 (ttmt) REVERT: F 248 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: F 380 ASP cc_start: 0.8514 (m-30) cc_final: 0.8301 (m-30) REVERT: F 425 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: G 105 LYS cc_start: 0.5075 (tptp) cc_final: 0.4132 (pttp) REVERT: G 124 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.5890 (tm) REVERT: G 146 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7570 (ttp-170) REVERT: G 149 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8196 (mmmt) REVERT: G 153 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7919 (mm-30) REVERT: G 202 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6811 (tm-30) REVERT: H 8 GLU cc_start: 0.5709 (mp0) cc_final: 0.4972 (tm-30) REVERT: H 38 GLU cc_start: 0.5771 (mt-10) cc_final: 0.5311 (pp20) REVERT: H 56 GLU cc_start: 0.6928 (pt0) cc_final: 0.5881 (pm20) REVERT: H 79 GLU cc_start: 0.6735 (tp30) cc_final: 0.6254 (tm-30) REVERT: H 89 TYR cc_start: 0.7538 (t80) cc_final: 0.7226 (t80) REVERT: I 93 GLU cc_start: 0.6305 (mm-30) cc_final: 0.5921 (mp0) REVERT: J 88 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7029 (ttp80) REVERT: J 96 GLN cc_start: 0.6201 (mt0) cc_final: 0.5532 (tp-100) REVERT: J 110 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6186 (tp30) REVERT: J 122 VAL cc_start: 0.4362 (OUTLIER) cc_final: 0.4008 (p) REVERT: J 150 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.4918 (mp) REVERT: J 162 GLN cc_start: 0.8256 (mt0) cc_final: 0.7865 (mp10) REVERT: J 172 ASP cc_start: 0.7177 (m-30) cc_final: 0.6834 (t70) REVERT: K 100 ARG cc_start: 0.6078 (ttm110) cc_final: 0.5449 (mtt180) REVERT: L 81 GLU cc_start: 0.7076 (tp30) cc_final: 0.6544 (mm-30) REVERT: L 82 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5903 (tm-30) REVERT: L 85 ARG cc_start: 0.6916 (ttp80) cc_final: 0.5753 (ttm170) REVERT: L 138 ARG cc_start: 0.6724 (mmm160) cc_final: 0.6212 (mmm160) REVERT: L 161 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8159 (t) outliers start: 61 outliers final: 33 residues processed: 310 average time/residue: 0.8489 time to fit residues: 300.3540 Evaluate side-chains 305 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 161 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 252 optimal weight: 0.9980 chunk 328 optimal weight: 2.9990 chunk 124 optimal weight: 0.0000 chunk 15 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 322 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN D 448 GLN F 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.093090 restraints weight = 43923.368| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.75 r_work: 0.2993 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30068 Z= 0.120 Angle : 0.525 8.768 40740 Z= 0.270 Chirality : 0.043 0.258 4567 Planarity : 0.005 0.060 5329 Dihedral : 5.851 146.432 4223 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.36 % Allowed : 17.72 % Favored : 80.92 % 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 are not related in a simple way. whole: 0.83 (0.14), residues: 3761 helix: 1.76 (0.13), residues: 1576 sheet: -0.21 (0.22), residues: 554 loop : -0.30 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 130 TYR 0.011 0.001 TYR G 133 PHE 0.014 0.001 PHE A 230 TRP 0.015 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00270 (30067) covalent geometry : angle 0.52456 (40740) hydrogen bonds : bond 0.04773 ( 1284) hydrogen bonds : angle 4.34008 ( 3687) Misc. bond : bond 0.00022 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10605.14 seconds wall clock time: 181 minutes 5.03 seconds (10865.03 seconds total)