Starting phenix.real_space_refine on Fri Mar 6 08:02:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vao_31854/03_2026/7vao_31854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vao_31854/03_2026/7vao_31854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vao_31854/03_2026/7vao_31854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vao_31854/03_2026/7vao_31854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vao_31854/03_2026/7vao_31854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vao_31854/03_2026/7vao_31854.map" } resolution = 3.4 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= 0.007 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 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 29558 Number of models: 1 Model: "" Number of chains: 15 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: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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: 6.85, per 1000 atoms: 0.23 Number of scatterers: 29558 At special positions: 0 Unit cell: (149.6, 139.92, 177.76, 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 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 25 sheets defined 46.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.867A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (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 295 through 317 removed outlier: 4.629A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.835A pdb=" N ALA A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.525A pdb=" N ASP A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.534A pdb=" N GLU A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.961A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix 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 543 through 550 removed outlier: 3.930A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.783A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (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 272 removed outlier: 3.799A pdb=" N PHE B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.945A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.644A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.781A 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: 4.103A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.864A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 542 through 550 removed outlier: 3.934A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.604A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.184A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.932A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 4.120A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.525A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.537A 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 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.240A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.970A 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 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.657A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.945A 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 574 removed outlier: 3.540A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 578 Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.865A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.532A pdb=" N LEU D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.971A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 removed outlier: 3.793A pdb=" N SER D 215 " --> pdb=" O GLY D 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'D' and resid 227 through 249 removed outlier: 3.526A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.593A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.517A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.577A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) 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: 3.862A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.657A 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: 4.504A pdb=" N ARG E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.851A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.608A 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 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 removed outlier: 4.191A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.073A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 445 through 446 No H-bonds generated for 'chain 'E' and resid 445 through 446' Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'E' and resid 466 through 470 removed outlier: 4.315A pdb=" N GLU E 469 " --> pdb=" O LYS E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.972A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.694A 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 120 through 124 removed outlier: 3.590A pdb=" N ARG F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) 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: 3.726A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.565A 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 361 through 365 Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.980A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 400 " --> pdb=" O VAL F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.538A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'G' and resid 7 through 68 removed outlier: 3.677A pdb=" N GLU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 207 removed outlier: 3.537A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 8 No H-bonds generated for 'chain 'H' and resid 6 through 8' Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 25 through 38 Processing helix chain 'H' and resid 54 through 59 removed outlier: 4.603A pdb=" N ALA H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) removed outlier: 3.804A 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 85 through 99 Processing helix chain 'I' and resid 82 through 104 removed outlier: 3.628A pdb=" N LYS I 97 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.623A pdb=" N GLU I 117 " --> pdb=" O LEU I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 removed outlier: 3.846A pdb=" N ALA J 93 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 115 removed outlier: 4.033A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.381A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 5.406A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.632A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.739A pdb=" N LEU L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 3.710A pdb=" N ARG L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 139 removed outlier: 4.311A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 3.926A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.336A 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: 6.584A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.247A 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: 5.614A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.735A 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: 6.641A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (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: 5.641A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (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: 5.726A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.804A 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 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.737A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.743A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 143 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 143 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 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 382 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 382 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: 3.880A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.797A 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: 6.734A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (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 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 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 143 through 148 removed outlier: 3.821A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 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 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 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: 6.529A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.625A 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: 6.977A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.583A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 93 removed outlier: 5.991A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET D 194 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.741A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 93 current: chain 'E' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 217 through 223 current: chain 'E' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 307 through 315 current: chain 'E' and resid 358 through 359 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.686A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.278A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC5, first strand: chain 'F' and resid 278 through 280 removed outlier: 6.366A pdb=" N TYR F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 90 through 96 removed outlier: 4.077A pdb=" N GLU G 90 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS G 105 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG G 103 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 22 removed outlier: 7.810A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1262 hydrogen bonds defined for protein. 3618 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: 5.22 Time building geometry restraints manager: 3.08 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: 9952 1.34 - 1.46: 3640 1.46 - 1.57: 16317 1.57 - 1.69: 11 1.69 - 1.80: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.467 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.479 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.480 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.495 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.453 0.057 2.00e-02 2.50e+03 8.22e+00 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 40516 2.62 - 5.25: 279 5.25 - 7.87: 16 7.87 - 10.49: 1 10.49 - 13.12: 1 Bond angle restraints: 40813 Sorted by residual: angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 119.90 106.78 13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" N ILE H 98 " pdb=" CA ILE H 98 " pdb=" C ILE H 98 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 angle pdb=" N GLY J 151 " pdb=" CA GLY J 151 " pdb=" C GLY J 151 " ideal model delta sigma weight residual 111.03 117.03 -6.00 1.87e+00 2.86e-01 1.03e+01 angle pdb=" CA LEU L 150 " pdb=" CB LEU L 150 " pdb=" CG LEU L 150 " ideal model delta sigma weight residual 116.30 126.79 -10.49 3.50e+00 8.16e-02 8.99e+00 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 110.34 2.86 9.60e-01 1.09e+00 8.86e+00 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 17509 24.95 - 49.90: 763 49.90 - 74.86: 84 74.86 - 99.81: 26 99.81 - 124.76: 1 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 64.76 -124.76 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" CA ARG A 23 " pdb=" C ARG A 23 " pdb=" N MET A 24 " pdb=" CA MET A 24 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 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 -122.38 62.37 1 2.00e+01 2.50e-03 1.29e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3598 0.051 - 0.102: 802 0.102 - 0.153: 168 0.153 - 0.204: 3 0.204 - 0.254: 1 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE B 211 " pdb=" CA ILE B 211 " pdb=" CG1 ILE B 211 " pdb=" CG2 ILE B 211 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PHE C 269 " pdb=" N PHE C 269 " pdb=" C PHE C 269 " pdb=" CB PHE C 269 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO E 324 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 269 " 0.012 2.00e-02 2.50e+03 1.42e-02 3.51e+00 pdb=" CG PHE C 269 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 269 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 269 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 269 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 269 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 269 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 226 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 227 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.025 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 551 2.70 - 3.25: 28854 3.25 - 3.80: 45942 3.80 - 4.35: 60001 4.35 - 4.90: 102511 Nonbonded interactions: 237859 Sorted by model distance: nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.144 3.040 nonbonded pdb=" NH2 ARG G 50 " pdb=" OE2 GLU G 144 " model vdw 2.151 3.120 nonbonded pdb=" O LEU B 241 " pdb=" OG SER B 245 " model vdw 2.156 3.040 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.158 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.161 3.040 ... (remaining 237854 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 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.890 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 30114 Z= 0.186 Angle : 0.562 13.117 40813 Z= 0.300 Chirality : 0.043 0.254 4572 Planarity : 0.004 0.047 5333 Dihedral : 13.723 124.761 11465 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.13 (0.14), residues: 3764 helix: 1.72 (0.14), residues: 1545 sheet: 0.02 (0.22), residues: 602 loop : 0.20 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.018 0.001 TYR B 184 PHE 0.032 0.001 PHE C 269 TRP 0.019 0.001 TRP A 330 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00415 (30114) covalent geometry : angle 0.56168 (40813) hydrogen bonds : bond 0.15353 ( 1262) hydrogen bonds : angle 5.77129 ( 3618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.7015 (ptm-80) REVERT: A 300 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 340 ARG cc_start: 0.6472 (mpt-90) cc_final: 0.5826 (mmm160) REVERT: A 447 TYR cc_start: 0.7518 (t80) cc_final: 0.7207 (t80) REVERT: A 491 ARG cc_start: 0.7214 (mtt-85) cc_final: 0.6590 (mtp-110) REVERT: A 530 ILE cc_start: 0.6208 (mm) cc_final: 0.5967 (tt) REVERT: A 550 ARG cc_start: 0.5551 (mmt180) cc_final: 0.5073 (mmp80) REVERT: A 553 TYR cc_start: 0.8571 (m-80) cc_final: 0.8256 (m-80) REVERT: B 109 HIS cc_start: 0.7759 (m-70) cc_final: 0.7410 (m-70) REVERT: B 143 PHE cc_start: 0.5089 (m-80) cc_final: 0.4734 (m-80) REVERT: B 169 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6417 (mm-30) REVERT: B 202 ASN cc_start: 0.7775 (m-40) cc_final: 0.7544 (m110) REVERT: B 243 LYS cc_start: 0.6707 (ttmt) cc_final: 0.6051 (ptpt) REVERT: B 244 TRP cc_start: 0.7697 (m100) cc_final: 0.7441 (m100) REVERT: B 284 ARG cc_start: 0.6844 (mtm180) cc_final: 0.6632 (ptp-170) REVERT: B 391 MET cc_start: 0.6330 (mtt) cc_final: 0.6063 (mmt) REVERT: B 441 GLU cc_start: 0.5832 (tp30) cc_final: 0.5046 (mt-10) REVERT: B 450 LEU cc_start: 0.5176 (tp) cc_final: 0.4875 (mm) REVERT: B 488 ARG cc_start: 0.5638 (ttp80) cc_final: 0.5247 (ttm110) REVERT: B 494 PHE cc_start: 0.6866 (t80) cc_final: 0.6607 (t80) REVERT: B 516 MET cc_start: 0.4666 (mtm) cc_final: 0.4207 (mtp) REVERT: B 518 MET cc_start: 0.6357 (mtp) cc_final: 0.5982 (mtt) REVERT: B 525 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6253 (mt-10) REVERT: B 567 MET cc_start: 0.5347 (mmm) cc_final: 0.4839 (mmt) REVERT: C 220 MET cc_start: 0.7587 (tpp) cc_final: 0.7367 (tpt) REVERT: C 347 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7333 (mt-10) REVERT: C 410 ASP cc_start: 0.7091 (t0) cc_final: 0.6810 (t70) REVERT: C 423 ASN cc_start: 0.8515 (t0) cc_final: 0.8278 (t0) REVERT: C 532 ARG cc_start: 0.5905 (ptt-90) cc_final: 0.5455 (ptm160) REVERT: D 50 VAL cc_start: 0.8682 (t) cc_final: 0.8312 (m) REVERT: D 62 GLU cc_start: 0.6608 (pm20) cc_final: 0.5794 (mp0) REVERT: D 67 ASP cc_start: 0.7480 (p0) cc_final: 0.7224 (p0) REVERT: D 237 MET cc_start: 0.7999 (mmt) cc_final: 0.7639 (mmt) REVERT: D 280 ARG cc_start: 0.6276 (ptm-80) cc_final: 0.5642 (ttp80) REVERT: D 380 ASP cc_start: 0.7003 (m-30) cc_final: 0.6454 (m-30) REVERT: D 456 LYS cc_start: 0.6889 (mmtt) cc_final: 0.6347 (mmmt) REVERT: E 78 ASP cc_start: 0.7442 (m-30) cc_final: 0.7164 (t0) REVERT: E 228 THR cc_start: 0.7801 (t) cc_final: 0.7577 (m) REVERT: E 373 GLU cc_start: 0.7407 (pm20) cc_final: 0.7065 (mp0) REVERT: E 390 VAL cc_start: 0.8018 (t) cc_final: 0.7763 (p) REVERT: E 399 ILE cc_start: 0.7047 (pt) cc_final: 0.6824 (mt) REVERT: E 405 THR cc_start: 0.7245 (p) cc_final: 0.6869 (p) REVERT: E 421 PHE cc_start: 0.6621 (m-80) cc_final: 0.6334 (m-80) REVERT: F 6 LYS cc_start: 0.7217 (tttt) cc_final: 0.6835 (mtmm) REVERT: F 53 GLU cc_start: 0.7489 (pt0) cc_final: 0.6893 (mm-30) REVERT: F 109 GLU cc_start: 0.7181 (tt0) cc_final: 0.6890 (tt0) REVERT: F 126 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7756 (ttpp) REVERT: F 210 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.6971 (ttt180) REVERT: F 280 ARG cc_start: 0.6659 (ttp-170) cc_final: 0.6309 (ttt90) REVERT: F 318 ASP cc_start: 0.7794 (p0) cc_final: 0.7233 (t0) REVERT: F 319 ASP cc_start: 0.8232 (m-30) cc_final: 0.7957 (m-30) REVERT: F 466 LYS cc_start: 0.7773 (mmmm) cc_final: 0.6977 (ptmt) REVERT: G 5 SER cc_start: 0.8061 (p) cc_final: 0.7684 (m) REVERT: G 155 LYS cc_start: 0.6388 (mttt) cc_final: 0.6035 (mttm) REVERT: G 156 LYS cc_start: 0.6595 (ttmm) cc_final: 0.5758 (tppt) REVERT: G 187 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6836 (tt0) REVERT: G 209 GLU cc_start: 0.3650 (mt-10) cc_final: 0.2796 (tp30) REVERT: H 1 MET cc_start: 0.4489 (mpp) cc_final: 0.3677 (mpp) REVERT: H 18 LEU cc_start: 0.4356 (mt) cc_final: 0.3932 (pp) REVERT: H 90 MET cc_start: 0.6110 (mmm) cc_final: 0.4827 (tmm) REVERT: J 84 ARG cc_start: 0.1892 (ptm160) cc_final: 0.1519 (ttt-90) REVERT: J 89 GLU cc_start: 0.5049 (tp30) cc_final: 0.4612 (mm-30) REVERT: L 173 ARG cc_start: 0.4537 (ttt90) cc_final: 0.4198 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.2194 time to fit residues: 200.5610 Evaluate side-chains 348 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN D 206 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN F 170 GLN F 413 GLN G 180 GLN J 124 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120569 restraints weight = 44643.258| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.42 r_work: 0.3173 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30114 Z= 0.260 Angle : 0.686 8.379 40813 Z= 0.352 Chirality : 0.049 0.263 4572 Planarity : 0.006 0.069 5333 Dihedral : 6.574 102.688 4259 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.62 % Allowed : 8.79 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.41 (0.14), residues: 3764 helix: 1.09 (0.13), residues: 1577 sheet: -0.11 (0.22), residues: 606 loop : -0.29 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 104 TYR 0.029 0.002 TYR D 13 PHE 0.031 0.002 PHE A 230 TRP 0.019 0.002 TRP C 119 HIS 0.009 0.002 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00639 (30114) covalent geometry : angle 0.68581 (40813) hydrogen bonds : bond 0.05718 ( 1262) hydrogen bonds : angle 4.77422 ( 3618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 347 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 530 ILE cc_start: 0.6691 (mm) cc_final: 0.6401 (tt) REVERT: B 109 HIS cc_start: 0.7803 (m-70) cc_final: 0.7524 (m170) REVERT: B 243 LYS cc_start: 0.7315 (ttmt) cc_final: 0.6801 (ptpt) REVERT: B 441 GLU cc_start: 0.6101 (tp30) cc_final: 0.5473 (mt-10) REVERT: B 450 LEU cc_start: 0.5766 (tp) cc_final: 0.5395 (mm) REVERT: B 518 MET cc_start: 0.7277 (mtp) cc_final: 0.7001 (mtt) REVERT: B 525 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6519 (mt-10) REVERT: B 567 MET cc_start: 0.5380 (mmm) cc_final: 0.4933 (mmt) REVERT: C 122 MET cc_start: 0.8153 (ttm) cc_final: 0.7941 (ttm) REVERT: C 450 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8407 (mp) REVERT: D 62 GLU cc_start: 0.6797 (pm20) cc_final: 0.6562 (pt0) REVERT: D 280 ARG cc_start: 0.6556 (ptm-80) cc_final: 0.6281 (ttp80) REVERT: D 456 LYS cc_start: 0.7252 (mmtt) cc_final: 0.6854 (mmmt) REVERT: E 110 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8132 (ttmm) REVERT: E 185 GLU cc_start: 0.5930 (pt0) cc_final: 0.5487 (pt0) REVERT: F 210 ARG cc_start: 0.7679 (ttp-110) cc_final: 0.7378 (ttt180) REVERT: F 416 ASP cc_start: 0.8291 (t0) cc_final: 0.8086 (t70) REVERT: F 466 LYS cc_start: 0.7942 (mmmm) cc_final: 0.7458 (mtpt) REVERT: G 5 SER cc_start: 0.8368 (p) cc_final: 0.8018 (m) REVERT: G 156 LYS cc_start: 0.7326 (ttmm) cc_final: 0.6461 (tppt) REVERT: G 166 GLN cc_start: 0.7561 (mm110) cc_final: 0.7359 (mm-40) REVERT: G 187 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7928 (tt0) REVERT: G 209 GLU cc_start: 0.3766 (mt-10) cc_final: 0.2657 (tp30) REVERT: H 1 MET cc_start: 0.5638 (mpp) cc_final: 0.4889 (mpp) REVERT: H 18 LEU cc_start: 0.5559 (mt) cc_final: 0.5182 (pp) REVERT: I 104 MET cc_start: 0.4067 (mtp) cc_final: 0.3820 (mtp) REVERT: L 138 ARG cc_start: 0.5560 (mtp85) cc_final: 0.5233 (mmm-85) REVERT: L 173 ARG cc_start: 0.4826 (ttt90) cc_final: 0.4510 (ttp-110) outliers start: 50 outliers final: 26 residues processed: 382 average time/residue: 0.2037 time to fit residues: 118.2765 Evaluate side-chains 319 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 49 optimal weight: 9.9990 chunk 118 optimal weight: 0.0050 chunk 270 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 251 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN D 249 HIS D 310 GLN F 166 GLN F 437 GLN G 180 GLN H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119719 restraints weight = 45635.760| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.39 r_work: 0.3213 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30114 Z= 0.110 Angle : 0.506 8.060 40813 Z= 0.260 Chirality : 0.043 0.175 4572 Planarity : 0.004 0.044 5333 Dihedral : 6.012 95.707 4259 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.49 % Allowed : 10.87 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.81 (0.14), residues: 3764 helix: 1.50 (0.14), residues: 1590 sheet: 0.02 (0.22), residues: 591 loop : -0.14 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 86 TYR 0.022 0.001 TYR D 13 PHE 0.018 0.001 PHE A 230 TRP 0.011 0.001 TRP A 330 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00244 (30114) covalent geometry : angle 0.50624 (40813) hydrogen bonds : bond 0.04147 ( 1262) hydrogen bonds : angle 4.33622 ( 3618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 324 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9195 (tttt) cc_final: 0.8885 (ptmm) REVERT: A 257 GLU cc_start: 0.7302 (tp30) cc_final: 0.6993 (tp30) REVERT: A 347 GLU cc_start: 0.7234 (tt0) cc_final: 0.7016 (tp30) REVERT: A 517 LYS cc_start: 0.8268 (tptp) cc_final: 0.7897 (tttt) REVERT: A 530 ILE cc_start: 0.6725 (mm) cc_final: 0.6387 (tt) REVERT: A 550 ARG cc_start: 0.6402 (mmt180) cc_final: 0.5565 (mmp80) REVERT: B 109 HIS cc_start: 0.8017 (m-70) cc_final: 0.7799 (m-70) REVERT: B 393 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6452 (tm-30) REVERT: B 441 GLU cc_start: 0.6298 (tp30) cc_final: 0.5530 (mt-10) REVERT: B 450 LEU cc_start: 0.5826 (tp) cc_final: 0.5342 (mm) REVERT: B 518 MET cc_start: 0.7152 (mtp) cc_final: 0.6713 (mtt) REVERT: B 525 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6483 (mt-10) REVERT: B 567 MET cc_start: 0.5436 (mmm) cc_final: 0.4797 (mmt) REVERT: C 450 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8375 (mp) REVERT: D 62 GLU cc_start: 0.6858 (pm20) cc_final: 0.6630 (pt0) REVERT: D 280 ARG cc_start: 0.6697 (ptm-80) cc_final: 0.6285 (ttp80) REVERT: D 456 LYS cc_start: 0.7075 (mmtt) cc_final: 0.6566 (mmmt) REVERT: E 110 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8108 (ttmm) REVERT: F 210 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7563 (ttt180) REVERT: F 420 ARG cc_start: 0.8325 (mtp-110) cc_final: 0.7912 (ttp80) REVERT: F 466 LYS cc_start: 0.7925 (mmmm) cc_final: 0.7461 (mtpt) REVERT: G 5 SER cc_start: 0.8508 (p) cc_final: 0.8175 (m) REVERT: G 156 LYS cc_start: 0.7283 (ttmm) cc_final: 0.6446 (tppt) REVERT: G 187 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7770 (tt0) REVERT: G 209 GLU cc_start: 0.3761 (mt-10) cc_final: 0.2889 (tp30) REVERT: H 1 MET cc_start: 0.5602 (mpp) cc_final: 0.4964 (mpp) REVERT: H 18 LEU cc_start: 0.4884 (mt) cc_final: 0.4670 (pp) REVERT: I 104 MET cc_start: 0.4108 (mtp) cc_final: 0.3890 (mtp) REVERT: J 89 GLU cc_start: 0.4055 (tp30) cc_final: 0.3126 (mm-30) REVERT: L 138 ARG cc_start: 0.5330 (mtp85) cc_final: 0.5053 (mmm-85) REVERT: L 173 ARG cc_start: 0.4900 (ttt90) cc_final: 0.4383 (mtm-85) outliers start: 46 outliers final: 19 residues processed: 360 average time/residue: 0.2076 time to fit residues: 114.2728 Evaluate side-chains 318 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 297 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain J residue 121 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 118 optimal weight: 0.0070 chunk 342 optimal weight: 30.0000 chunk 239 optimal weight: 10.0000 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 145 HIS E 222 ASN E 427 GLN G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116537 restraints weight = 45435.324| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.45 r_work: 0.3166 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30114 Z= 0.208 Angle : 0.602 8.321 40813 Z= 0.307 Chirality : 0.046 0.179 4572 Planarity : 0.005 0.050 5333 Dihedral : 6.264 98.847 4259 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.04 % Allowed : 12.49 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.46 (0.14), residues: 3764 helix: 1.23 (0.13), residues: 1582 sheet: -0.15 (0.22), residues: 587 loop : -0.36 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 491 TYR 0.024 0.002 TYR D 13 PHE 0.026 0.002 PHE A 230 TRP 0.012 0.002 TRP D 471 HIS 0.008 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00510 (30114) covalent geometry : angle 0.60242 (40813) hydrogen bonds : bond 0.04952 ( 1262) hydrogen bonds : angle 4.47553 ( 3618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 291 time to evaluate : 0.848 Fit side-chains REVERT: A 8 LYS cc_start: 0.9138 (tttt) cc_final: 0.8785 (ptmm) REVERT: A 257 GLU cc_start: 0.7366 (tp30) cc_final: 0.7163 (tp30) REVERT: A 517 LYS cc_start: 0.8364 (tptp) cc_final: 0.7989 (tttt) REVERT: A 530 ILE cc_start: 0.6794 (mm) cc_final: 0.6448 (tt) REVERT: B 244 TRP cc_start: 0.8162 (m100) cc_final: 0.7923 (m-90) REVERT: B 441 GLU cc_start: 0.6147 (tp30) cc_final: 0.5394 (mt-10) REVERT: B 450 LEU cc_start: 0.5901 (tp) cc_final: 0.5411 (mm) REVERT: B 518 MET cc_start: 0.7165 (mtp) cc_final: 0.6938 (mtt) REVERT: B 525 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6528 (mt-10) REVERT: B 567 MET cc_start: 0.5474 (mmm) cc_final: 0.5180 (mmt) REVERT: C 450 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8371 (mp) REVERT: D 62 GLU cc_start: 0.6895 (pm20) cc_final: 0.6684 (pt0) REVERT: D 280 ARG cc_start: 0.6745 (ptm-80) cc_final: 0.6366 (ttp80) REVERT: D 456 LYS cc_start: 0.7508 (mmtt) cc_final: 0.6837 (mmmt) REVERT: E 110 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8185 (ttmm) REVERT: E 185 GLU cc_start: 0.5949 (pt0) cc_final: 0.5495 (pt0) REVERT: E 287 MET cc_start: 0.8585 (ttp) cc_final: 0.8379 (ttp) REVERT: E 320 ASP cc_start: 0.6832 (t0) cc_final: 0.5852 (p0) REVERT: F 210 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7584 (ttt180) REVERT: G 5 SER cc_start: 0.8436 (p) cc_final: 0.8116 (m) REVERT: G 156 LYS cc_start: 0.7372 (ttmm) cc_final: 0.6526 (tppt) REVERT: G 187 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7893 (tt0) REVERT: G 209 GLU cc_start: 0.3310 (mt-10) cc_final: 0.2529 (tp30) REVERT: H 1 MET cc_start: 0.5369 (mpp) cc_final: 0.4552 (mpp) REVERT: I 104 MET cc_start: 0.3835 (mtp) cc_final: 0.3630 (mtp) REVERT: J 89 GLU cc_start: 0.3896 (tp30) cc_final: 0.2845 (mm-30) REVERT: L 61 GLU cc_start: 0.3361 (pm20) cc_final: 0.2388 (mm-30) REVERT: L 138 ARG cc_start: 0.5134 (mtp85) cc_final: 0.4773 (mmm-85) REVERT: L 173 ARG cc_start: 0.4810 (ttt90) cc_final: 0.4215 (ttt-90) outliers start: 63 outliers final: 42 residues processed: 339 average time/residue: 0.1883 time to fit residues: 100.3248 Evaluate side-chains 323 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 0.4980 chunk 189 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 348 optimal weight: 0.0010 chunk 37 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN G 180 GLN J 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118211 restraints weight = 45574.354| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.45 r_work: 0.3192 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30114 Z= 0.132 Angle : 0.523 7.691 40813 Z= 0.267 Chirality : 0.043 0.173 4572 Planarity : 0.004 0.047 5333 Dihedral : 5.981 94.475 4259 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.04 % Allowed : 13.56 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.61 (0.14), residues: 3764 helix: 1.41 (0.13), residues: 1583 sheet: -0.13 (0.22), residues: 594 loop : -0.32 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 488 TYR 0.023 0.001 TYR B 428 PHE 0.021 0.001 PHE A 230 TRP 0.009 0.001 TRP A 330 HIS 0.005 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00309 (30114) covalent geometry : angle 0.52326 (40813) hydrogen bonds : bond 0.04186 ( 1262) hydrogen bonds : angle 4.29314 ( 3618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 293 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9136 (tttt) cc_final: 0.8832 (ptmm) REVERT: A 53 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: A 517 LYS cc_start: 0.8320 (tptp) cc_final: 0.7971 (tttt) REVERT: A 530 ILE cc_start: 0.6786 (mm) cc_final: 0.6436 (tt) REVERT: A 550 ARG cc_start: 0.6161 (mmt180) cc_final: 0.5355 (mmp80) REVERT: B 211 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6509 (tp) REVERT: B 391 MET cc_start: 0.5987 (OUTLIER) cc_final: 0.5535 (mtt) REVERT: B 441 GLU cc_start: 0.6247 (tp30) cc_final: 0.5433 (mt-10) REVERT: B 450 LEU cc_start: 0.5909 (tp) cc_final: 0.5542 (mm) REVERT: B 518 MET cc_start: 0.7065 (mtp) cc_final: 0.6841 (mtt) REVERT: B 525 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6434 (mt-10) REVERT: B 567 MET cc_start: 0.5450 (mmm) cc_final: 0.5132 (mmt) REVERT: C 79 MET cc_start: 0.8511 (mtm) cc_final: 0.8302 (mtm) REVERT: C 450 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8369 (mp) REVERT: D 62 GLU cc_start: 0.6900 (pm20) cc_final: 0.6667 (pt0) REVERT: D 280 ARG cc_start: 0.6767 (ptm-80) cc_final: 0.6357 (ttp80) REVERT: D 456 LYS cc_start: 0.7530 (mmtt) cc_final: 0.6872 (mmmt) REVERT: E 110 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8168 (ttmm) REVERT: E 185 GLU cc_start: 0.5950 (pt0) cc_final: 0.5436 (pt0) REVERT: F 210 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7570 (ttt180) REVERT: F 420 ARG cc_start: 0.8433 (mtp-110) cc_final: 0.8107 (ttp80) REVERT: G 5 SER cc_start: 0.8451 (p) cc_final: 0.8148 (m) REVERT: G 156 LYS cc_start: 0.7342 (ttmm) cc_final: 0.6574 (tppt) REVERT: G 187 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7745 (tt0) REVERT: H 1 MET cc_start: 0.5330 (mpp) cc_final: 0.4627 (mpp) REVERT: J 89 GLU cc_start: 0.3961 (tp30) cc_final: 0.2898 (mm-30) REVERT: J 149 ARG cc_start: 0.4426 (mtm180) cc_final: 0.3826 (mmm160) REVERT: J 186 LEU cc_start: 0.4180 (OUTLIER) cc_final: 0.3757 (mp) REVERT: L 61 GLU cc_start: 0.3484 (pm20) cc_final: 0.2483 (mm-30) REVERT: L 138 ARG cc_start: 0.4992 (mtp85) cc_final: 0.4762 (mmm-85) REVERT: L 173 ARG cc_start: 0.4783 (ttt90) cc_final: 0.4085 (ttt180) outliers start: 63 outliers final: 40 residues processed: 339 average time/residue: 0.1863 time to fit residues: 98.8334 Evaluate side-chains 325 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain L residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 158 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 571 GLN F 166 GLN F 413 GLN G 17 GLN G 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117317 restraints weight = 45520.802| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.42 r_work: 0.3161 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 30114 Z= 0.226 Angle : 0.621 7.603 40813 Z= 0.317 Chirality : 0.047 0.185 4572 Planarity : 0.005 0.066 5333 Dihedral : 6.391 99.899 4259 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.89 % Allowed : 14.08 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.21 (0.14), residues: 3764 helix: 1.08 (0.13), residues: 1576 sheet: -0.31 (0.22), residues: 586 loop : -0.55 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 86 TYR 0.024 0.002 TYR D 13 PHE 0.027 0.002 PHE A 230 TRP 0.017 0.002 TRP D 471 HIS 0.008 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00555 (30114) covalent geometry : angle 0.62065 (40813) hydrogen bonds : bond 0.05118 ( 1262) hydrogen bonds : angle 4.53005 ( 3618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 288 time to evaluate : 1.056 Fit side-chains REVERT: A 53 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: A 257 GLU cc_start: 0.7505 (tp30) cc_final: 0.7266 (tp30) REVERT: A 323 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7750 (mmt) REVERT: A 461 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: A 517 LYS cc_start: 0.8406 (tptp) cc_final: 0.8059 (tttt) REVERT: A 530 ILE cc_start: 0.6776 (mm) cc_final: 0.6342 (tt) REVERT: A 550 ARG cc_start: 0.6209 (mmt180) cc_final: 0.5347 (mmp80) REVERT: B 211 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6562 (tp) REVERT: B 391 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5423 (mtt) REVERT: B 393 GLU cc_start: 0.7058 (tp30) cc_final: 0.6701 (tm-30) REVERT: B 441 GLU cc_start: 0.6161 (tp30) cc_final: 0.5393 (mt-10) REVERT: B 518 MET cc_start: 0.7012 (mtp) cc_final: 0.6754 (mtt) REVERT: B 525 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6458 (mt-10) REVERT: B 567 MET cc_start: 0.5359 (mmm) cc_final: 0.5063 (mmt) REVERT: C 450 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 467 ILE cc_start: 0.7421 (mm) cc_final: 0.7208 (mt) REVERT: D 62 GLU cc_start: 0.6998 (pm20) cc_final: 0.6755 (pt0) REVERT: D 280 ARG cc_start: 0.6914 (ptm-80) cc_final: 0.6415 (ttp80) REVERT: D 437 GLN cc_start: 0.8150 (tt0) cc_final: 0.7900 (mt0) REVERT: D 456 LYS cc_start: 0.7698 (mmtt) cc_final: 0.6975 (mmmt) REVERT: E 110 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8183 (ttmm) REVERT: E 185 GLU cc_start: 0.5962 (pt0) cc_final: 0.5660 (pt0) REVERT: E 320 ASP cc_start: 0.6971 (t0) cc_final: 0.6366 (p0) REVERT: F 210 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7654 (ttt180) REVERT: G 5 SER cc_start: 0.8498 (p) cc_final: 0.8214 (m) REVERT: G 156 LYS cc_start: 0.7442 (ttmm) cc_final: 0.6586 (tppt) REVERT: G 187 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7880 (tt0) REVERT: G 192 PHE cc_start: 0.8415 (t80) cc_final: 0.8048 (t80) REVERT: H 18 LEU cc_start: 0.4092 (pp) cc_final: 0.3427 (mt) REVERT: J 89 GLU cc_start: 0.4028 (tp30) cc_final: 0.2824 (mm-30) REVERT: J 149 ARG cc_start: 0.4492 (mtm180) cc_final: 0.3810 (mmm160) REVERT: J 186 LEU cc_start: 0.4130 (OUTLIER) cc_final: 0.3793 (mp) REVERT: K 104 MET cc_start: 0.3241 (ttt) cc_final: 0.1732 (mmm) REVERT: L 61 GLU cc_start: 0.3702 (pm20) cc_final: 0.2618 (mm-30) REVERT: L 173 ARG cc_start: 0.4724 (ttt90) cc_final: 0.4026 (ttt180) outliers start: 89 outliers final: 57 residues processed: 355 average time/residue: 0.1862 time to fit residues: 104.4423 Evaluate side-chains 337 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 272 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 303 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 371 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 313 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 397 GLN B 469 GLN E 161 ASN F 166 GLN G 10 ASN G 17 GLN G 180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118974 restraints weight = 45388.464| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.34 r_work: 0.3182 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30114 Z= 0.165 Angle : 0.561 8.524 40813 Z= 0.286 Chirality : 0.044 0.178 4572 Planarity : 0.005 0.050 5333 Dihedral : 6.219 97.895 4259 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.66 % Allowed : 14.99 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.30 (0.14), residues: 3764 helix: 1.20 (0.13), residues: 1577 sheet: -0.34 (0.22), residues: 590 loop : -0.53 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 488 TYR 0.024 0.001 TYR B 428 PHE 0.024 0.002 PHE A 230 TRP 0.010 0.001 TRP D 471 HIS 0.006 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00397 (30114) covalent geometry : angle 0.56060 (40813) hydrogen bonds : bond 0.04570 ( 1262) hydrogen bonds : angle 4.42296 ( 3618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 0.970 Fit side-chains REVERT: A 53 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: A 323 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7671 (mmt) REVERT: A 530 ILE cc_start: 0.6884 (mm) cc_final: 0.6445 (tt) REVERT: A 550 ARG cc_start: 0.6104 (mmt180) cc_final: 0.5290 (mmp80) REVERT: B 202 ASN cc_start: 0.6926 (m110) cc_final: 0.6684 (m110) REVERT: B 211 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6493 (tp) REVERT: B 441 GLU cc_start: 0.6205 (tp30) cc_final: 0.5444 (mt-10) REVERT: B 518 MET cc_start: 0.7036 (mtp) cc_final: 0.6755 (mtt) REVERT: B 525 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6533 (mt-10) REVERT: B 567 MET cc_start: 0.5299 (mmm) cc_final: 0.5020 (mmt) REVERT: C 19 MET cc_start: 0.8602 (mmm) cc_final: 0.8311 (mtp) REVERT: C 450 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8368 (mp) REVERT: C 467 ILE cc_start: 0.7362 (mm) cc_final: 0.7064 (mt) REVERT: D 62 GLU cc_start: 0.6854 (pm20) cc_final: 0.6635 (pt0) REVERT: D 280 ARG cc_start: 0.6886 (ptm-80) cc_final: 0.6381 (ttp80) REVERT: D 437 GLN cc_start: 0.8100 (tt0) cc_final: 0.7873 (mt0) REVERT: D 456 LYS cc_start: 0.7701 (mmtt) cc_final: 0.6972 (mmmt) REVERT: E 110 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8205 (ttmm) REVERT: E 185 GLU cc_start: 0.5817 (pt0) cc_final: 0.5557 (pt0) REVERT: E 320 ASP cc_start: 0.6944 (t0) cc_final: 0.6388 (p0) REVERT: F 210 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7549 (ttt180) REVERT: F 420 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.7914 (ttp80) REVERT: G 5 SER cc_start: 0.8479 (p) cc_final: 0.8003 (m) REVERT: G 10 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8063 (m110) REVERT: G 156 LYS cc_start: 0.7380 (ttmm) cc_final: 0.6555 (tppt) REVERT: G 187 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7826 (tt0) REVERT: H 18 LEU cc_start: 0.4176 (pp) cc_final: 0.3553 (mt) REVERT: J 89 GLU cc_start: 0.3940 (tp30) cc_final: 0.2787 (mm-30) REVERT: J 121 LEU cc_start: 0.3954 (OUTLIER) cc_final: 0.3740 (tt) REVERT: J 149 ARG cc_start: 0.4506 (mtm180) cc_final: 0.3821 (mmm160) REVERT: J 186 LEU cc_start: 0.4142 (OUTLIER) cc_final: 0.3824 (mp) REVERT: K 104 MET cc_start: 0.3142 (ttt) cc_final: 0.1652 (mmm) REVERT: L 61 GLU cc_start: 0.3535 (pm20) cc_final: 0.2550 (mm-30) REVERT: L 86 ARG cc_start: 0.5008 (mtp180) cc_final: 0.4562 (mtm180) REVERT: L 143 GLN cc_start: 0.3728 (OUTLIER) cc_final: 0.3062 (tm-30) REVERT: L 173 ARG cc_start: 0.4695 (ttt90) cc_final: 0.4090 (ttt-90) outliers start: 82 outliers final: 63 residues processed: 350 average time/residue: 0.1847 time to fit residues: 102.2302 Evaluate side-chains 348 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 316 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 330 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 347 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN G 10 ASN G 17 GLN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116266 restraints weight = 45706.609| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.39 r_work: 0.3177 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30114 Z= 0.192 Angle : 0.583 9.616 40813 Z= 0.297 Chirality : 0.045 0.182 4572 Planarity : 0.005 0.051 5333 Dihedral : 6.317 98.921 4259 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.08 % Allowed : 14.79 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.21 (0.14), residues: 3764 helix: 1.12 (0.13), residues: 1578 sheet: -0.36 (0.22), residues: 584 loop : -0.58 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 488 TYR 0.024 0.002 TYR B 428 PHE 0.039 0.002 PHE G 192 TRP 0.013 0.001 TRP D 471 HIS 0.007 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00467 (30114) covalent geometry : angle 0.58306 (40813) hydrogen bonds : bond 0.04766 ( 1262) hydrogen bonds : angle 4.47023 ( 3618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 280 time to evaluate : 1.044 Fit side-chains REVERT: A 53 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: A 323 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7674 (mmt) REVERT: A 461 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: A 530 ILE cc_start: 0.6830 (mm) cc_final: 0.6401 (tt) REVERT: A 550 ARG cc_start: 0.6056 (mmt180) cc_final: 0.5246 (mmp80) REVERT: B 202 ASN cc_start: 0.6894 (m110) cc_final: 0.6628 (m110) REVERT: B 211 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6465 (tp) REVERT: B 441 GLU cc_start: 0.6119 (tp30) cc_final: 0.5416 (mt-10) REVERT: B 518 MET cc_start: 0.7027 (mtp) cc_final: 0.6726 (mtt) REVERT: B 525 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6394 (mt-10) REVERT: B 567 MET cc_start: 0.5262 (mmm) cc_final: 0.4995 (mmt) REVERT: C 19 MET cc_start: 0.8565 (mmm) cc_final: 0.8347 (mtp) REVERT: C 288 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8514 (mt) REVERT: C 450 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 467 ILE cc_start: 0.7360 (mm) cc_final: 0.7051 (mt) REVERT: D 62 GLU cc_start: 0.6822 (pm20) cc_final: 0.6567 (pt0) REVERT: D 280 ARG cc_start: 0.6867 (ptm-80) cc_final: 0.6359 (ttp80) REVERT: D 437 GLN cc_start: 0.8095 (tt0) cc_final: 0.7860 (mt0) REVERT: D 456 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7023 (mmmt) REVERT: E 110 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8191 (ttmm) REVERT: E 185 GLU cc_start: 0.5885 (pt0) cc_final: 0.5639 (pt0) REVERT: E 320 ASP cc_start: 0.6885 (t0) cc_final: 0.6434 (p0) REVERT: F 210 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7579 (ttt180) REVERT: G 5 SER cc_start: 0.8499 (p) cc_final: 0.8145 (m) REVERT: G 156 LYS cc_start: 0.7342 (ttmm) cc_final: 0.6490 (tppt) REVERT: G 187 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7838 (tt0) REVERT: J 89 GLU cc_start: 0.4095 (tp30) cc_final: 0.3019 (pt0) REVERT: J 121 LEU cc_start: 0.3819 (OUTLIER) cc_final: 0.3568 (tt) REVERT: J 149 ARG cc_start: 0.4554 (mtm180) cc_final: 0.3875 (mmm160) REVERT: J 186 LEU cc_start: 0.4136 (OUTLIER) cc_final: 0.3822 (mp) REVERT: K 104 MET cc_start: 0.3193 (ttt) cc_final: 0.1722 (mmm) REVERT: L 61 GLU cc_start: 0.3625 (pm20) cc_final: 0.2537 (mm-30) REVERT: L 143 GLN cc_start: 0.3644 (OUTLIER) cc_final: 0.2822 (tm-30) REVERT: L 173 ARG cc_start: 0.4634 (ttt90) cc_final: 0.3978 (ttt-90) outliers start: 95 outliers final: 69 residues processed: 360 average time/residue: 0.1839 time to fit residues: 105.0087 Evaluate side-chains 349 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 270 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 371 optimal weight: 10.0000 chunk 370 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN G 10 ASN G 17 GLN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120970 restraints weight = 44999.915| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.25 r_work: 0.3209 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30114 Z= 0.178 Angle : 0.571 9.759 40813 Z= 0.291 Chirality : 0.045 0.181 4572 Planarity : 0.005 0.050 5333 Dihedral : 6.422 98.495 4259 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.89 % Allowed : 15.18 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.22 (0.14), residues: 3764 helix: 1.14 (0.13), residues: 1577 sheet: -0.34 (0.22), residues: 584 loop : -0.58 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 86 TYR 0.023 0.001 TYR B 428 PHE 0.038 0.002 PHE G 192 TRP 0.013 0.001 TRP D 471 HIS 0.007 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00432 (30114) covalent geometry : angle 0.57069 (40813) hydrogen bonds : bond 0.04625 ( 1262) hydrogen bonds : angle 4.43525 ( 3618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 278 time to evaluate : 1.108 Fit side-chains REVERT: A 53 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: A 257 GLU cc_start: 0.7255 (tp30) cc_final: 0.7043 (tp30) REVERT: A 323 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7584 (mmt) REVERT: A 530 ILE cc_start: 0.6863 (mm) cc_final: 0.6410 (tt) REVERT: A 550 ARG cc_start: 0.6124 (mmt180) cc_final: 0.5294 (mmp80) REVERT: B 211 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6427 (tp) REVERT: B 441 GLU cc_start: 0.6177 (tp30) cc_final: 0.5427 (mt-10) REVERT: B 518 MET cc_start: 0.7067 (mtp) cc_final: 0.6640 (mtt) REVERT: B 525 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6547 (mt-10) REVERT: B 567 MET cc_start: 0.5394 (mmm) cc_final: 0.5121 (mmt) REVERT: C 19 MET cc_start: 0.8589 (mmm) cc_final: 0.8298 (mtp) REVERT: C 450 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8395 (mp) REVERT: C 467 ILE cc_start: 0.7371 (mm) cc_final: 0.7043 (mt) REVERT: D 62 GLU cc_start: 0.6798 (pm20) cc_final: 0.6485 (pt0) REVERT: D 280 ARG cc_start: 0.6862 (ptm-80) cc_final: 0.6159 (ttp80) REVERT: D 437 GLN cc_start: 0.8183 (tt0) cc_final: 0.7976 (mt0) REVERT: D 456 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7035 (mmmt) REVERT: E 110 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8192 (ttmm) REVERT: E 320 ASP cc_start: 0.6801 (t0) cc_final: 0.6541 (p0) REVERT: F 210 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7523 (ttt180) REVERT: F 420 ARG cc_start: 0.8487 (mtp-110) cc_final: 0.7948 (ttp80) REVERT: G 156 LYS cc_start: 0.7344 (ttmm) cc_final: 0.6497 (tppt) REVERT: G 187 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7838 (tt0) REVERT: H 18 LEU cc_start: 0.5229 (OUTLIER) cc_final: 0.4574 (mt) REVERT: J 89 GLU cc_start: 0.4061 (tp30) cc_final: 0.3792 (tp30) REVERT: J 121 LEU cc_start: 0.4008 (OUTLIER) cc_final: 0.3620 (tt) REVERT: J 186 LEU cc_start: 0.4316 (OUTLIER) cc_final: 0.4011 (mp) REVERT: K 104 MET cc_start: 0.3416 (ttt) cc_final: 0.1867 (mmm) REVERT: L 61 GLU cc_start: 0.3384 (pm20) cc_final: 0.2330 (mm-30) REVERT: L 85 ARG cc_start: 0.4601 (ptm-80) cc_final: 0.3720 (ttp80) REVERT: L 86 ARG cc_start: 0.4694 (mtp180) cc_final: 0.4163 (mtm180) REVERT: L 143 GLN cc_start: 0.3611 (OUTLIER) cc_final: 0.2950 (tm-30) REVERT: L 173 ARG cc_start: 0.4678 (ttt90) cc_final: 0.3944 (ttt180) outliers start: 89 outliers final: 69 residues processed: 351 average time/residue: 0.1866 time to fit residues: 102.8100 Evaluate side-chains 350 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 272 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 295 optimal weight: 3.9990 chunk 339 optimal weight: 30.0000 chunk 288 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 325 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 272 optimal weight: 10.0000 chunk 286 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN C 316 GLN G 180 GLN L 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.146744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121421 restraints weight = 44876.044| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.41 r_work: 0.3234 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30114 Z= 0.105 Angle : 0.501 9.603 40813 Z= 0.256 Chirality : 0.042 0.178 4572 Planarity : 0.004 0.049 5333 Dihedral : 5.940 89.856 4259 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.82 % Allowed : 16.32 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.57 (0.14), residues: 3764 helix: 1.44 (0.14), residues: 1585 sheet: -0.19 (0.22), residues: 600 loop : -0.42 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 488 TYR 0.020 0.001 TYR D 13 PHE 0.035 0.001 PHE G 192 TRP 0.013 0.001 TRP B 244 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00237 (30114) covalent geometry : angle 0.50108 (40813) hydrogen bonds : bond 0.03744 ( 1262) hydrogen bonds : angle 4.18507 ( 3618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 291 time to evaluate : 1.075 Fit side-chains REVERT: A 53 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: A 257 GLU cc_start: 0.7218 (tp30) cc_final: 0.6965 (tp30) REVERT: A 550 ARG cc_start: 0.6077 (mmt180) cc_final: 0.5269 (mmp80) REVERT: B 211 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6360 (tp) REVERT: B 441 GLU cc_start: 0.6246 (tp30) cc_final: 0.5468 (mt-10) REVERT: B 488 ARG cc_start: 0.6131 (ttp80) cc_final: 0.5554 (ttm110) REVERT: B 518 MET cc_start: 0.7002 (mtp) cc_final: 0.6575 (mtt) REVERT: B 525 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6615 (mt-10) REVERT: B 567 MET cc_start: 0.5331 (mmm) cc_final: 0.5062 (mmt) REVERT: C 19 MET cc_start: 0.8559 (mmm) cc_final: 0.8339 (mtp) REVERT: C 450 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8368 (mp) REVERT: D 62 GLU cc_start: 0.6705 (pm20) cc_final: 0.6399 (pt0) REVERT: D 280 ARG cc_start: 0.6757 (ptm-80) cc_final: 0.6263 (ttp80) REVERT: D 437 GLN cc_start: 0.7977 (tt0) cc_final: 0.7762 (mt0) REVERT: D 456 LYS cc_start: 0.7619 (mmtt) cc_final: 0.6966 (mmmt) REVERT: E 320 ASP cc_start: 0.6792 (t0) cc_final: 0.6502 (p0) REVERT: F 420 ARG cc_start: 0.8434 (mtp-110) cc_final: 0.7950 (ttp80) REVERT: G 156 LYS cc_start: 0.7280 (ttmm) cc_final: 0.6503 (tppt) REVERT: G 187 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7765 (tt0) REVERT: H 18 LEU cc_start: 0.5068 (pp) cc_final: 0.4409 (mt) REVERT: H 90 MET cc_start: 0.5581 (mmt) cc_final: 0.5208 (mmt) REVERT: J 89 GLU cc_start: 0.4003 (tp30) cc_final: 0.2889 (mm-30) REVERT: J 121 LEU cc_start: 0.3879 (OUTLIER) cc_final: 0.3368 (tt) REVERT: J 186 LEU cc_start: 0.4252 (OUTLIER) cc_final: 0.3902 (mp) REVERT: K 104 MET cc_start: 0.3342 (ttt) cc_final: 0.1883 (mmm) REVERT: L 61 GLU cc_start: 0.3403 (pm20) cc_final: 0.2333 (mm-30) REVERT: L 85 ARG cc_start: 0.4692 (ptm-80) cc_final: 0.3779 (ttp80) REVERT: L 86 ARG cc_start: 0.4747 (mtp180) cc_final: 0.4230 (mtm180) REVERT: L 173 ARG cc_start: 0.4653 (ttt90) cc_final: 0.3954 (ttt180) outliers start: 56 outliers final: 41 residues processed: 336 average time/residue: 0.1882 time to fit residues: 99.7522 Evaluate side-chains 319 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 31 optimal weight: 8.9990 chunk 361 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 367 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 chunk 181 optimal weight: 0.0030 chunk 226 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121725 restraints weight = 44897.166| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.32 r_work: 0.3239 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 30114 Z= 0.157 Angle : 0.625 59.196 40813 Z= 0.352 Chirality : 0.043 0.251 4572 Planarity : 0.004 0.049 5333 Dihedral : 5.953 90.160 4259 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.65 % Allowed : 16.51 % Favored : 81.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % 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: 0.55 (0.14), residues: 3764 helix: 1.42 (0.13), residues: 1587 sheet: -0.18 (0.22), residues: 600 loop : -0.42 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 488 TYR 0.020 0.001 TYR D 13 PHE 0.031 0.001 PHE G 192 TRP 0.012 0.001 TRP B 244 HIS 0.005 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00353 (30114) covalent geometry : angle 0.62512 (40813) hydrogen bonds : bond 0.03840 ( 1262) hydrogen bonds : angle 4.19224 ( 3618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6596.17 seconds wall clock time: 113 minutes 26.70 seconds (6806.70 seconds total)