Starting phenix.real_space_refine on Tue May 27 02:56:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gxy_34365/05_2025/8gxy_34365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gxy_34365/05_2025/8gxy_34365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gxy_34365/05_2025/8gxy_34365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gxy_34365/05_2025/8gxy_34365.map" model { file = "/net/cci-nas-00/data/ceres_data/8gxy_34365/05_2025/8gxy_34365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gxy_34365/05_2025/8gxy_34365.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 18705 2.51 5 N 5116 2.21 5 O 5546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29472 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.04, per 1000 atoms: 0.54 Number of scatterers: 29472 At special positions: 0 Unit cell: (147.42, 147.42, 175.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 5546 8.00 N 5116 7.00 C 18705 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: 7.29 Conformation dependent library (CDL) restraints added in 3.8 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: 147 helices and 26 sheets defined 47.7% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.551A pdb=" N ILE A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.908A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.121A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.894A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.736A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.128A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.257A 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 removed outlier: 3.627A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.518A pdb=" N LEU A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.804A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.779A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.512A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.920A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.669A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.954A pdb=" N LEU B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 542 through 550 removed outlier: 4.070A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.716A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (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 245 Processing helix chain 'C' and resid 259 through 269 removed outlier: 3.588A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (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: 4.171A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.053A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 352 No H-bonds generated for 'chain 'C' and resid 351 through 352' Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 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: 3.896A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.982A 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 540 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.574A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.776A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.758A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.949A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 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 'D' and resid 467 through 472 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.882A pdb=" N MET E 88 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.506A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.722A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 212 through 215 removed outlier: 3.926A pdb=" N SER E 215 " --> pdb=" O GLY E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 250 removed outlier: 4.478A pdb=" N ARG E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.699A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.534A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.500A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.841A 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 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.636A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 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 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.623A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 347 Processing helix chain 'F' and resid 359 through 365 removed outlier: 4.379A pdb=" N ASN F 363 " --> pdb=" O ARG F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.611A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 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: 3.517A 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 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.672A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.534A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 167 removed outlier: 3.724A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.732A pdb=" N ARG H 39 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 6.245A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 removed outlier: 4.020A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 119 removed outlier: 3.856A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 64 through 94 removed outlier: 4.021A pdb=" N VAL J 68 " --> pdb=" O GLY J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 115 removed outlier: 4.027A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.802A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 3.942A pdb=" N ASP J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.839A 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 94 Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 127 through 130 Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 167 through 188 removed outlier: 5.389A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 5.640A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (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: 6.414A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (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: 6.477A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.844A 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: 5.762A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.771A 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: 5.755A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (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: 5.813A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.518A 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: 5.978A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.559A 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 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 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 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 3.840A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.875A 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: 6.687A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 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 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 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 422 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: 6.613A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.533A 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 129 removed outlier: 6.668A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 204 through 205 removed outlier: 4.835A pdb=" N VAL B 218 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 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 382 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.393A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.739A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.571A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.996A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AC1, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.559A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.962A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR E 258 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA E 192 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.506A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC5, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.737A pdb=" N ARG F 91 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.549A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 95 Processing sheet with id=AC8, first strand: chain 'H' and resid 19 through 21 removed outlier: 6.427A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1332 hydrogen bonds defined for protein. 3807 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: 9.98 Time building geometry restraints manager: 8.35 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: 9947 1.34 - 1.46: 4218 1.46 - 1.57: 15664 1.57 - 1.69: 0 1.69 - 1.81: 194 Bond restraints: 30023 Sorted by residual: bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.451 0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" O2 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.453 0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.454 0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" O1 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.454 0.044 2.00e-02 2.50e+03 4.92e+00 bond pdb=" O3 SO4 C 600 " pdb=" S SO4 C 600 " ideal model delta sigma weight residual 1.499 1.457 0.042 2.00e-02 2.50e+03 4.51e+00 ... (remaining 30018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 39415 1.22 - 2.45: 973 2.45 - 3.67: 201 3.67 - 4.90: 74 4.90 - 6.12: 7 Bond angle restraints: 40670 Sorted by residual: angle pdb=" N ILE E 100 " pdb=" CA ILE E 100 " pdb=" C ILE E 100 " ideal model delta sigma weight residual 113.20 109.61 3.59 9.60e-01 1.09e+00 1.40e+01 angle pdb=" CA GLU B 564 " pdb=" CB GLU B 564 " pdb=" CG GLU B 564 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.36e+00 angle pdb=" N GLU B 564 " pdb=" CA GLU B 564 " pdb=" CB GLU B 564 " ideal model delta sigma weight residual 110.28 114.65 -4.37 1.55e+00 4.16e-01 7.96e+00 angle pdb=" C PHE B 563 " pdb=" N GLU B 564 " pdb=" CA GLU B 564 " ideal model delta sigma weight residual 120.31 116.09 4.22 1.52e+00 4.33e-01 7.72e+00 angle pdb=" N GLY B 228 " pdb=" CA GLY B 228 " pdb=" C GLY B 228 " ideal model delta sigma weight residual 112.34 117.55 -5.21 2.04e+00 2.40e-01 6.52e+00 ... (remaining 40665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16562 17.98 - 35.96: 1360 35.96 - 53.95: 280 53.95 - 71.93: 58 71.93 - 89.91: 44 Dihedral angle restraints: 18304 sinusoidal: 7482 harmonic: 10822 Sorted by residual: dihedral pdb=" CA TYR F 8 " pdb=" C TYR F 8 " pdb=" N THR F 9 " pdb=" CA THR F 9 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLU B 363 " pdb=" C GLU B 363 " pdb=" N ARG B 364 " pdb=" CA ARG B 364 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA VAL F 21 " pdb=" C VAL F 21 " pdb=" N GLU F 22 " pdb=" CA GLU F 22 " ideal model delta harmonic sigma weight residual 180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2614 0.030 - 0.060: 1307 0.060 - 0.090: 346 0.090 - 0.119: 252 0.119 - 0.149: 41 Chirality restraints: 4560 Sorted by residual: chirality pdb=" CA ILE A 83 " pdb=" N ILE A 83 " pdb=" C ILE A 83 " pdb=" CB ILE A 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO D 317 " pdb=" N PRO D 317 " pdb=" C PRO D 317 " pdb=" CB PRO D 317 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE D 337 " pdb=" N ILE D 337 " pdb=" C ILE D 337 " pdb=" CB ILE D 337 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 4557 not shown) Planarity restraints: 5330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 145 " -0.047 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO J 146 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO J 146 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 146 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 386 " -0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO C 387 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 387 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 387 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 170 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 171 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " -0.025 5.00e-02 4.00e+02 ... (remaining 5327 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 171 2.54 - 3.13: 23005 3.13 - 3.72: 45011 3.72 - 4.31: 65147 4.31 - 4.90: 111053 Nonbonded interactions: 244387 Sorted by model distance: nonbonded pdb=" OG SER F 51 " pdb=" OE1 GLU F 53 " model vdw 1.951 3.040 nonbonded pdb=" O LYS E 370 " pdb=" OG1 THR E 371 " model vdw 1.993 3.040 nonbonded pdb=" NH2 ARG B 481 " pdb=" OE2 GLU B 485 " model vdw 2.003 3.120 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.026 3.040 nonbonded pdb=" O LYS D 370 " pdb=" OG1 THR D 371 " model vdw 2.029 3.040 ... (remaining 244382 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' 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: 0.010 Normalize map: mean=0, sd=1: 1.650 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: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.890 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30023 Z= 0.211 Angle : 0.520 6.120 40670 Z= 0.273 Chirality : 0.043 0.149 4560 Planarity : 0.004 0.073 5330 Dihedral : 14.570 89.908 11386 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 0.03 % Allowed : 7.98 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3764 helix: 1.65 (0.14), residues: 1552 sheet: -0.29 (0.21), residues: 591 loop : 0.10 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 119 HIS 0.005 0.001 HIS B 283 PHE 0.014 0.002 PHE B 563 TYR 0.019 0.001 TYR D 331 ARG 0.005 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.14095 ( 1332) hydrogen bonds : angle 6.05019 ( 3807) covalent geometry : bond 0.00498 (30023) covalent geometry : angle 0.51956 (40670) *********************** 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 833 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 832 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7856 (mttt) cc_final: 0.7470 (mmmt) REVERT: A 43 ASP cc_start: 0.8109 (t0) cc_final: 0.7859 (t70) REVERT: A 109 HIS cc_start: 0.7748 (m-70) cc_final: 0.7300 (m170) REVERT: A 169 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7370 (tp30) REVERT: A 181 LEU cc_start: 0.8243 (mt) cc_final: 0.8030 (mt) REVERT: A 191 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7525 (ttp80) REVERT: A 257 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 264 ASP cc_start: 0.7065 (m-30) cc_final: 0.6857 (m-30) REVERT: A 456 GLU cc_start: 0.7356 (tt0) cc_final: 0.7095 (tm-30) REVERT: A 498 ASN cc_start: 0.8874 (t0) cc_final: 0.8629 (t0) REVERT: A 571 GLN cc_start: 0.6814 (mm-40) cc_final: 0.6549 (tt0) REVERT: B 19 MET cc_start: 0.8468 (mmm) cc_final: 0.8265 (mmm) REVERT: B 93 ARG cc_start: 0.7297 (mtp180) cc_final: 0.7071 (mmp80) REVERT: B 122 MET cc_start: 0.8459 (mtm) cc_final: 0.8222 (mtt) REVERT: B 154 ARG cc_start: 0.6787 (mtp-110) cc_final: 0.6531 (ptp90) REVERT: B 158 LYS cc_start: 0.7674 (tttt) cc_final: 0.7276 (tttt) REVERT: B 166 TYR cc_start: 0.8506 (m-80) cc_final: 0.8100 (m-80) REVERT: B 197 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.6976 (ttt-90) REVERT: B 200 ASP cc_start: 0.7194 (m-30) cc_final: 0.6805 (m-30) REVERT: B 276 LYS cc_start: 0.7543 (mmtt) cc_final: 0.7105 (mtmt) REVERT: B 391 MET cc_start: 0.7012 (mmp) cc_final: 0.6743 (mmt) REVERT: B 474 ASP cc_start: 0.6823 (m-30) cc_final: 0.6161 (t0) REVERT: B 524 LYS cc_start: 0.7711 (tttt) cc_final: 0.7329 (mppt) REVERT: C 29 LYS cc_start: 0.8555 (mttp) cc_final: 0.8238 (mptt) REVERT: C 59 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8071 (mtmm) REVERT: C 180 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6656 (mm-30) REVERT: C 191 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7930 (mtm180) REVERT: C 268 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6560 (tt0) REVERT: C 374 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7561 (mt-10) REVERT: C 410 ASP cc_start: 0.8103 (t0) cc_final: 0.7857 (t70) REVERT: C 412 SER cc_start: 0.8395 (m) cc_final: 0.8117 (t) REVERT: D 98 LYS cc_start: 0.7277 (tttt) cc_final: 0.6778 (mmtp) REVERT: D 128 GLU cc_start: 0.7778 (pt0) cc_final: 0.7564 (pp20) REVERT: D 162 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7507 (mt-10) REVERT: D 260 MET cc_start: 0.8409 (mmm) cc_final: 0.8082 (mmm) REVERT: D 305 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7831 (mttp) REVERT: D 398 ILE cc_start: 0.7878 (mt) cc_final: 0.7546 (mm) REVERT: D 413 GLN cc_start: 0.7628 (mt0) cc_final: 0.7297 (mt0) REVERT: D 428 GLN cc_start: 0.8068 (mt0) cc_final: 0.7793 (mt0) REVERT: D 450 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6354 (mm-30) REVERT: D 453 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7724 (mtt90) REVERT: E 98 LYS cc_start: 0.7613 (mttt) cc_final: 0.7297 (mmtp) REVERT: E 115 THR cc_start: 0.8330 (p) cc_final: 0.7960 (t) REVERT: E 194 MET cc_start: 0.7840 (mpp) cc_final: 0.7505 (mpp) REVERT: E 216 ARG cc_start: 0.7898 (ptt90) cc_final: 0.7469 (ptt-90) REVERT: E 222 ASN cc_start: 0.8493 (t0) cc_final: 0.8280 (t0) REVERT: E 274 ARG cc_start: 0.7463 (mtp180) cc_final: 0.6278 (mmp-170) REVERT: E 304 LYS cc_start: 0.8378 (mttm) cc_final: 0.8089 (mttm) REVERT: E 368 LYS cc_start: 0.7361 (mtpt) cc_final: 0.6928 (mtmm) REVERT: E 394 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7797 (mttp) REVERT: E 409 ARG cc_start: 0.7261 (ttm170) cc_final: 0.6942 (ttm110) REVERT: F 6 LYS cc_start: 0.7503 (tttt) cc_final: 0.6751 (pttt) REVERT: F 79 VAL cc_start: 0.8514 (p) cc_final: 0.8032 (m) REVERT: F 81 ARG cc_start: 0.8371 (mtt90) cc_final: 0.8066 (mmt90) REVERT: F 98 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7560 (mptm) REVERT: F 126 LYS cc_start: 0.8239 (tttm) cc_final: 0.7943 (tttp) REVERT: F 265 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6734 (tm-30) REVERT: F 393 ARG cc_start: 0.8262 (mtt180) cc_final: 0.8016 (mtt180) REVERT: F 416 ASP cc_start: 0.8053 (t0) cc_final: 0.7760 (t0) REVERT: F 437 GLN cc_start: 0.8117 (tt0) cc_final: 0.7765 (tt0) REVERT: G 17 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7380 (mm110) REVERT: G 38 GLU cc_start: 0.7268 (tt0) cc_final: 0.6853 (tp30) REVERT: G 48 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6538 (mt-10) REVERT: G 148 LYS cc_start: 0.7185 (mttt) cc_final: 0.6856 (mtpt) REVERT: G 149 LYS cc_start: 0.7740 (mmmm) cc_final: 0.7393 (mmtm) REVERT: G 152 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6992 (mm-30) REVERT: G 156 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7303 (mttt) REVERT: G 159 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.7145 (mtm110) REVERT: G 165 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8033 (mt-10) REVERT: G 202 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6762 (mt-10) REVERT: H 15 LEU cc_start: 0.5797 (tp) cc_final: 0.5584 (tp) REVERT: J 76 ARG cc_start: 0.6287 (mtp85) cc_final: 0.5466 (ttm170) REVERT: J 105 ARG cc_start: 0.4856 (mtt180) cc_final: 0.4530 (mmt-90) REVERT: J 109 LEU cc_start: 0.6182 (tp) cc_final: 0.5792 (mt) REVERT: J 121 LEU cc_start: 0.4965 (tp) cc_final: 0.4567 (mm) REVERT: J 160 LYS cc_start: 0.6584 (mmtt) cc_final: 0.6017 (mtmm) REVERT: L 84 ARG cc_start: 0.6328 (ttm-80) cc_final: 0.6058 (ttm170) REVERT: L 132 GLU cc_start: 0.3956 (mt-10) cc_final: 0.3676 (tp30) REVERT: L 160 LYS cc_start: 0.6849 (mttp) cc_final: 0.5987 (mmtp) REVERT: L 162 GLN cc_start: 0.7403 (pt0) cc_final: 0.6400 (pt0) REVERT: L 181 LYS cc_start: 0.6083 (mttm) cc_final: 0.5573 (mtpt) outliers start: 1 outliers final: 2 residues processed: 832 average time/residue: 1.8660 time to fit residues: 1746.1248 Evaluate side-chains 512 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 510 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 8.9990 chunk 282 optimal weight: 0.5980 chunk 156 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 0.0470 chunk 338 optimal weight: 8.9990 overall best weight: 1.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 239 GLN A 316 GLN A 469 GLN B 397 GLN C 316 GLN C 397 GLN D 252 HIS D 427 GLN E 142 ASN E 166 GLN E 338 GLN E 364 ASN E 427 GLN E 458 HIS F 142 ASN F 161 ASN F 206 GLN F 262 ASN F 323 HIS F 363 ASN F 429 ASN G 68 GLN L 162 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.144708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.108228 restraints weight = 32386.722| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.37 r_work: 0.2964 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30023 Z= 0.151 Angle : 0.558 10.539 40670 Z= 0.289 Chirality : 0.045 0.175 4560 Planarity : 0.005 0.062 5330 Dihedral : 4.585 60.952 4185 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.22 % Rotamer: Outliers : 3.24 % Allowed : 13.88 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3764 helix: 1.79 (0.14), residues: 1575 sheet: -0.18 (0.22), residues: 580 loop : 0.26 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS A 185 PHE 0.017 0.002 PHE E 414 TYR 0.015 0.002 TYR F 349 ARG 0.008 0.001 ARG H 66 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 1332) hydrogen bonds : angle 4.79881 ( 3807) covalent geometry : bond 0.00352 (30023) covalent geometry : angle 0.55765 (40670) *********************** 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 611 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 511 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8392 (mttt) cc_final: 0.8165 (mmmt) REVERT: A 53 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: A 109 HIS cc_start: 0.7969 (m-70) cc_final: 0.7715 (m-70) REVERT: A 156 ARG cc_start: 0.6562 (ttp80) cc_final: 0.6174 (ttp80) REVERT: A 191 ARG cc_start: 0.8077 (mtp180) cc_final: 0.7835 (ttp80) REVERT: A 323 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8579 (mpp) REVERT: A 340 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7271 (mpt-90) REVERT: A 445 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 449 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: A 498 ASN cc_start: 0.8886 (t0) cc_final: 0.8654 (t0) REVERT: A 536 ILE cc_start: 0.7303 (tt) cc_final: 0.6754 (pp) REVERT: A 571 GLN cc_start: 0.6782 (mm-40) cc_final: 0.6573 (tt0) REVERT: B 19 MET cc_start: 0.8794 (mmm) cc_final: 0.8269 (mmm) REVERT: B 32 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: B 122 MET cc_start: 0.8239 (mtm) cc_final: 0.7983 (mtt) REVERT: B 130 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7094 (ptm-80) REVERT: B 154 ARG cc_start: 0.7047 (mtp-110) cc_final: 0.6798 (ptp90) REVERT: B 158 LYS cc_start: 0.7662 (tttt) cc_final: 0.7249 (tttt) REVERT: B 325 ASP cc_start: 0.7423 (t0) cc_final: 0.7205 (t70) REVERT: B 391 MET cc_start: 0.7395 (mmp) cc_final: 0.7059 (mmt) REVERT: B 474 ASP cc_start: 0.6863 (m-30) cc_final: 0.5962 (t0) REVERT: C 29 LYS cc_start: 0.8837 (mttp) cc_final: 0.8569 (mptt) REVERT: C 112 ASP cc_start: 0.8230 (t0) cc_final: 0.7963 (t0) REVERT: C 170 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6524 (mm-30) REVERT: C 180 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6808 (mm-30) REVERT: C 191 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8239 (mtm180) REVERT: C 268 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7149 (tt0) REVERT: C 342 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: C 393 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: C 547 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7307 (tpp80) REVERT: D 98 LYS cc_start: 0.7839 (tttt) cc_final: 0.7429 (mmtp) REVERT: D 162 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: D 236 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8375 (mtt90) REVERT: D 248 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7553 (mm-30) REVERT: D 305 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8079 (mttp) REVERT: D 398 ILE cc_start: 0.8152 (mt) cc_final: 0.7731 (mm) REVERT: D 413 GLN cc_start: 0.7930 (mt0) cc_final: 0.7711 (mt0) REVERT: D 450 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6656 (mm-30) REVERT: D 453 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7857 (mtt90) REVERT: D 457 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6163 (m-30) REVERT: E 26 ASP cc_start: 0.7438 (m-30) cc_final: 0.7230 (m-30) REVERT: E 61 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6827 (pt0) REVERT: E 98 LYS cc_start: 0.7915 (mttt) cc_final: 0.7706 (mmtp) REVERT: E 200 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7996 (mt-10) REVERT: E 216 ARG cc_start: 0.8281 (ptt90) cc_final: 0.7908 (ptt-90) REVERT: E 274 ARG cc_start: 0.7927 (mtp180) cc_final: 0.6824 (mmp-170) REVERT: E 368 LYS cc_start: 0.7491 (mtpt) cc_final: 0.7147 (mtmm) REVERT: E 388 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8094 (t0) REVERT: E 394 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8097 (mttp) REVERT: F 6 LYS cc_start: 0.7680 (tttt) cc_final: 0.7034 (pttt) REVERT: F 25 LYS cc_start: 0.7131 (ptmm) cc_final: 0.6844 (mtpt) REVERT: F 53 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7450 (mm-30) REVERT: F 79 VAL cc_start: 0.8762 (p) cc_final: 0.8446 (m) REVERT: F 81 ARG cc_start: 0.8601 (mtt90) cc_final: 0.8348 (mmt90) REVERT: F 98 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8055 (mmtp) REVERT: F 210 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7657 (ttt-90) REVERT: F 265 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7647 (tm-30) REVERT: F 437 GLN cc_start: 0.8750 (tt0) cc_final: 0.8339 (tt0) REVERT: F 456 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7705 (mmmt) REVERT: F 465 GLN cc_start: 0.7604 (tt0) cc_final: 0.7388 (tt0) REVERT: G 38 GLU cc_start: 0.7794 (tt0) cc_final: 0.7516 (tp30) REVERT: G 47 MET cc_start: 0.7077 (tpp) cc_final: 0.6769 (mpp) REVERT: G 48 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6346 (mt-10) REVERT: G 139 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.5908 (ttm170) REVERT: G 148 LYS cc_start: 0.7415 (mttt) cc_final: 0.7024 (mtpt) REVERT: G 149 LYS cc_start: 0.7909 (mmmm) cc_final: 0.7626 (mmtp) REVERT: G 156 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7782 (mtmt) REVERT: G 159 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7830 (mtm110) REVERT: G 166 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7045 (mt0) REVERT: G 198 LYS cc_start: 0.8087 (tttt) cc_final: 0.7462 (mmtt) REVERT: H 36 LEU cc_start: 0.5275 (tt) cc_final: 0.4882 (pp) REVERT: H 90 MET cc_start: 0.6801 (tpp) cc_final: 0.6504 (tpp) REVERT: J 72 ARG cc_start: 0.4556 (ttp-110) cc_final: 0.4171 (mtt180) REVERT: J 105 ARG cc_start: 0.4982 (mtt180) cc_final: 0.4517 (mmt-90) REVERT: J 109 LEU cc_start: 0.6175 (tp) cc_final: 0.5875 (mt) REVERT: J 121 LEU cc_start: 0.4619 (tp) cc_final: 0.4281 (mm) REVERT: L 74 GLN cc_start: 0.6796 (tp40) cc_final: 0.6230 (tp40) REVERT: L 76 ARG cc_start: 0.6882 (mtp85) cc_final: 0.6649 (mtp180) REVERT: L 84 ARG cc_start: 0.6273 (ttm-80) cc_final: 0.5846 (ttm170) REVERT: L 153 ARG cc_start: 0.5766 (ttm170) cc_final: 0.5506 (ttp80) REVERT: L 160 LYS cc_start: 0.7356 (mttp) cc_final: 0.6426 (mmtp) REVERT: L 162 GLN cc_start: 0.7596 (pt0) cc_final: 0.6540 (pt0) outliers start: 100 outliers final: 31 residues processed: 571 average time/residue: 1.8242 time to fit residues: 1174.8571 Evaluate side-chains 484 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 436 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 332 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 313 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN C 283 HIS ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN D 428 GLN E 129 GLN E 132 GLN F 206 GLN F 222 ASN F 363 ASN G 175 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.140850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.103791 restraints weight = 32631.948| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.45 r_work: 0.2872 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30023 Z= 0.222 Angle : 0.620 9.877 40670 Z= 0.321 Chirality : 0.047 0.161 4560 Planarity : 0.006 0.061 5330 Dihedral : 4.907 61.578 4185 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.99 % Favored : 97.98 % Rotamer: Outliers : 4.44 % Allowed : 14.60 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3764 helix: 1.60 (0.13), residues: 1583 sheet: -0.18 (0.22), residues: 583 loop : 0.17 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 119 HIS 0.005 0.001 HIS F 344 PHE 0.020 0.002 PHE E 414 TYR 0.017 0.002 TYR B 523 ARG 0.008 0.001 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.05469 ( 1332) hydrogen bonds : angle 4.82422 ( 3807) covalent geometry : bond 0.00540 (30023) covalent geometry : angle 0.62019 (40670) *********************** 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 587 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 450 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8439 (mttt) cc_final: 0.8107 (mmmt) REVERT: A 53 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: A 109 HIS cc_start: 0.7914 (m-70) cc_final: 0.7538 (m170) REVERT: A 115 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8116 (tttp) REVERT: A 138 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8024 (p) REVERT: A 340 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7402 (mpt-90) REVERT: A 445 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: A 449 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 469 GLN cc_start: 0.7475 (mt0) cc_final: 0.6990 (mm110) REVERT: A 498 ASN cc_start: 0.8888 (t0) cc_final: 0.8683 (t0) REVERT: A 571 GLN cc_start: 0.6667 (mm-40) cc_final: 0.6427 (tt0) REVERT: B 19 MET cc_start: 0.8853 (mmm) cc_final: 0.8392 (mmm) REVERT: B 32 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: B 93 ARG cc_start: 0.7903 (mmp80) cc_final: 0.7217 (mmm160) REVERT: B 122 MET cc_start: 0.8246 (mtm) cc_final: 0.7941 (mtt) REVERT: B 124 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7034 (mppt) REVERT: B 130 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7166 (ptm-80) REVERT: B 154 ARG cc_start: 0.7161 (mtp-110) cc_final: 0.6902 (ptp90) REVERT: B 156 ARG cc_start: 0.7148 (mtp85) cc_final: 0.6288 (tpp80) REVERT: B 158 LYS cc_start: 0.7635 (tttt) cc_final: 0.7434 (tttp) REVERT: B 170 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7208 (mt-10) REVERT: B 276 LYS cc_start: 0.7461 (mmtt) cc_final: 0.7253 (mtmt) REVERT: B 391 MET cc_start: 0.7497 (mmp) cc_final: 0.7255 (mmt) REVERT: B 410 ASP cc_start: 0.8641 (p0) cc_final: 0.8360 (p0) REVERT: B 474 ASP cc_start: 0.7103 (m-30) cc_final: 0.6078 (t0) REVERT: B 509 MET cc_start: 0.8982 (mmm) cc_final: 0.8525 (mmm) REVERT: B 524 LYS cc_start: 0.7648 (mttp) cc_final: 0.7105 (mppt) REVERT: C 29 LYS cc_start: 0.8955 (mttp) cc_final: 0.8723 (mmtp) REVERT: C 180 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6862 (mm-30) REVERT: C 191 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8399 (mtm180) REVERT: C 268 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7260 (tt0) REVERT: C 336 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7962 (tp30) REVERT: C 342 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: C 547 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6925 (tpt90) REVERT: D 52 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: D 98 LYS cc_start: 0.7888 (tttt) cc_final: 0.7225 (mtpt) REVERT: D 162 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: D 280 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7833 (ttp-110) REVERT: D 373 GLU cc_start: 0.7663 (pm20) cc_final: 0.7180 (pt0) REVERT: D 398 ILE cc_start: 0.8217 (mt) cc_final: 0.7843 (mm) REVERT: D 413 GLN cc_start: 0.8052 (mt0) cc_final: 0.7798 (mt0) REVERT: D 450 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6660 (mm-30) REVERT: D 453 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7866 (mtt180) REVERT: E 26 ASP cc_start: 0.7694 (m-30) cc_final: 0.7387 (m-30) REVERT: E 61 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6807 (pt0) REVERT: E 98 LYS cc_start: 0.8128 (mttt) cc_final: 0.7829 (mmtp) REVERT: E 200 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8215 (mt-10) REVERT: E 207 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: E 216 ARG cc_start: 0.8335 (ptt90) cc_final: 0.7922 (ptt-90) REVERT: E 274 ARG cc_start: 0.7994 (mtp180) cc_final: 0.6876 (mmp-170) REVERT: E 388 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8281 (t0) REVERT: E 394 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8094 (mttp) REVERT: E 445 MET cc_start: 0.8621 (mtp) cc_final: 0.8417 (mtp) REVERT: F 25 LYS cc_start: 0.7197 (ptmm) cc_final: 0.6890 (mtpt) REVERT: F 53 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7498 (mm-30) REVERT: F 79 VAL cc_start: 0.8803 (p) cc_final: 0.8509 (m) REVERT: F 98 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8054 (mmtp) REVERT: F 125 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7449 (ttm170) REVERT: F 210 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7729 (ttt-90) REVERT: F 259 ASP cc_start: 0.7138 (t0) cc_final: 0.6923 (t70) REVERT: F 265 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7838 (tm-30) REVERT: F 373 GLU cc_start: 0.7700 (mp0) cc_final: 0.7286 (pm20) REVERT: F 394 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7677 (mttt) REVERT: F 413 GLN cc_start: 0.8508 (mt0) cc_final: 0.8254 (mt0) REVERT: F 437 GLN cc_start: 0.8836 (tt0) cc_final: 0.8495 (tt0) REVERT: F 456 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7613 (mmmt) REVERT: F 465 GLN cc_start: 0.7694 (tt0) cc_final: 0.7037 (pt0) REVERT: G 38 GLU cc_start: 0.7926 (tt0) cc_final: 0.7623 (tp30) REVERT: G 47 MET cc_start: 0.7170 (tpp) cc_final: 0.6730 (mpp) REVERT: G 48 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6346 (mt-10) REVERT: G 139 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6106 (ttm170) REVERT: G 148 LYS cc_start: 0.7495 (mttt) cc_final: 0.7157 (mtpm) REVERT: G 156 LYS cc_start: 0.8379 (mtpp) cc_final: 0.7847 (mttt) REVERT: G 159 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.7808 (mtm110) REVERT: G 166 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: G 198 LYS cc_start: 0.8284 (tttt) cc_final: 0.7527 (mptt) REVERT: H 1 MET cc_start: 0.5288 (OUTLIER) cc_final: 0.5075 (ptm) REVERT: H 15 LEU cc_start: 0.5737 (tp) cc_final: 0.5472 (tp) REVERT: H 19 GLU cc_start: 0.4274 (tp30) cc_final: 0.4028 (tp30) REVERT: H 36 LEU cc_start: 0.5371 (tt) cc_final: 0.4854 (pp) REVERT: H 44 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6686 (tp) REVERT: H 90 MET cc_start: 0.6895 (tpp) cc_final: 0.6515 (tpp) REVERT: J 105 ARG cc_start: 0.4772 (mtt180) cc_final: 0.4405 (mmt-90) REVERT: J 109 LEU cc_start: 0.6200 (tp) cc_final: 0.5774 (mt) REVERT: J 121 LEU cc_start: 0.4678 (tp) cc_final: 0.4225 (mm) REVERT: J 126 GLU cc_start: 0.4429 (OUTLIER) cc_final: 0.4065 (mp0) REVERT: L 74 GLN cc_start: 0.6725 (tp40) cc_final: 0.6272 (tp40) REVERT: L 76 ARG cc_start: 0.6769 (mtp85) cc_final: 0.6447 (mtt180) REVERT: L 84 ARG cc_start: 0.6244 (ttm-80) cc_final: 0.5990 (ttm170) REVERT: L 153 ARG cc_start: 0.5977 (ttm170) cc_final: 0.5718 (ttp80) REVERT: L 160 LYS cc_start: 0.7359 (mttp) cc_final: 0.6510 (mmtp) REVERT: L 162 GLN cc_start: 0.7611 (pt0) cc_final: 0.6665 (pt0) outliers start: 137 outliers final: 52 residues processed: 535 average time/residue: 1.8631 time to fit residues: 1127.6671 Evaluate side-chains 500 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 423 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 217 optimal weight: 0.7980 chunk 243 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 244 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 354 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN D 428 GLN E 129 GLN E 363 ASN E 413 GLN F 129 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.142647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.105595 restraints weight = 32804.293| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.49 r_work: 0.2918 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30023 Z= 0.127 Angle : 0.517 10.439 40670 Z= 0.267 Chirality : 0.043 0.185 4560 Planarity : 0.005 0.046 5330 Dihedral : 4.571 60.709 4185 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.65 % Favored : 98.33 % Rotamer: Outliers : 3.31 % Allowed : 16.35 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.14), residues: 3764 helix: 1.84 (0.13), residues: 1573 sheet: -0.16 (0.21), residues: 580 loop : 0.28 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 119 HIS 0.003 0.001 HIS C 418 PHE 0.015 0.001 PHE C 559 TYR 0.016 0.001 TYR H 89 ARG 0.005 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 1332) hydrogen bonds : angle 4.56961 ( 3807) covalent geometry : bond 0.00295 (30023) covalent geometry : angle 0.51652 (40670) *********************** 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 551 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 449 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8405 (mttt) cc_final: 0.8101 (mmmt) REVERT: A 53 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: A 109 HIS cc_start: 0.7875 (m-70) cc_final: 0.7649 (m-70) REVERT: A 191 ARG cc_start: 0.8126 (mtp180) cc_final: 0.7828 (ttp80) REVERT: A 340 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7203 (mpt-90) REVERT: A 445 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: A 449 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: A 498 ASN cc_start: 0.8832 (t0) cc_final: 0.8619 (t0) REVERT: A 571 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6440 (tt0) REVERT: B 19 MET cc_start: 0.8839 (mmm) cc_final: 0.8334 (mmm) REVERT: B 32 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: B 93 ARG cc_start: 0.7868 (mmp80) cc_final: 0.7243 (mmm160) REVERT: B 122 MET cc_start: 0.8205 (mtm) cc_final: 0.7954 (mtt) REVERT: B 124 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7024 (mppt) REVERT: B 130 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7122 (ptm-80) REVERT: B 154 ARG cc_start: 0.7057 (mtp-110) cc_final: 0.6842 (ptp90) REVERT: B 170 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7160 (mt-10) REVERT: B 391 MET cc_start: 0.7491 (mmp) cc_final: 0.7240 (mmt) REVERT: B 410 ASP cc_start: 0.8515 (p0) cc_final: 0.8222 (p0) REVERT: B 467 ILE cc_start: 0.7362 (mt) cc_final: 0.7033 (tp) REVERT: B 474 ASP cc_start: 0.7057 (m-30) cc_final: 0.6030 (t0) REVERT: B 524 LYS cc_start: 0.7583 (mttp) cc_final: 0.7066 (mppt) REVERT: B 541 GLN cc_start: 0.6414 (OUTLIER) cc_final: 0.5963 (mt0) REVERT: C 3 GLN cc_start: 0.7706 (tt0) cc_final: 0.7411 (tp40) REVERT: C 29 LYS cc_start: 0.8896 (mttp) cc_final: 0.8681 (mmtp) REVERT: C 156 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6919 (mmm-85) REVERT: C 180 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6810 (mm-30) REVERT: C 336 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7829 (tp30) REVERT: C 342 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: C 410 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8243 (t0) REVERT: C 547 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7236 (tpp80) REVERT: D 52 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: D 62 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5816 (mt-10) REVERT: D 98 LYS cc_start: 0.7902 (tttt) cc_final: 0.7229 (mtpt) REVERT: D 128 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7294 (pp20) REVERT: D 162 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: D 236 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8323 (mtt90) REVERT: D 248 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7504 (mm-30) REVERT: D 280 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7859 (ttp-110) REVERT: D 373 GLU cc_start: 0.7624 (pm20) cc_final: 0.7223 (pm20) REVERT: D 398 ILE cc_start: 0.8270 (mt) cc_final: 0.7951 (mm) REVERT: D 413 GLN cc_start: 0.7953 (mt0) cc_final: 0.7692 (mt0) REVERT: D 420 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7467 (mmt-90) REVERT: D 450 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6641 (mm-30) REVERT: D 453 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7822 (mtt180) REVERT: D 457 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6025 (m-30) REVERT: E 26 ASP cc_start: 0.7641 (m-30) cc_final: 0.7335 (m-30) REVERT: E 61 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: E 98 LYS cc_start: 0.8074 (mttt) cc_final: 0.7801 (mmtp) REVERT: E 200 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8126 (mt-10) REVERT: E 207 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: E 211 THR cc_start: 0.8511 (p) cc_final: 0.8269 (m) REVERT: E 216 ARG cc_start: 0.8318 (ptt90) cc_final: 0.7897 (ptt-90) REVERT: E 274 ARG cc_start: 0.7930 (mtp180) cc_final: 0.6835 (mmp-170) REVERT: E 388 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8186 (t0) REVERT: E 394 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8059 (mttp) REVERT: F 4 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6815 (pp) REVERT: F 25 LYS cc_start: 0.7177 (ptmm) cc_final: 0.6900 (mtpt) REVERT: F 53 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7500 (mm-30) REVERT: F 79 VAL cc_start: 0.8739 (p) cc_final: 0.8504 (m) REVERT: F 98 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7858 (mmtp) REVERT: F 125 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7302 (ttm170) REVERT: F 265 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7783 (tm-30) REVERT: F 373 GLU cc_start: 0.7578 (mp0) cc_final: 0.7213 (pm20) REVERT: F 394 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7611 (mttt) REVERT: F 437 GLN cc_start: 0.8804 (tt0) cc_final: 0.8502 (tt0) REVERT: F 456 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7613 (mmmt) REVERT: F 465 GLN cc_start: 0.7634 (tt0) cc_final: 0.7034 (pt0) REVERT: G 38 GLU cc_start: 0.7878 (tt0) cc_final: 0.7586 (tp30) REVERT: G 47 MET cc_start: 0.7142 (tpp) cc_final: 0.6890 (tpp) REVERT: G 48 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6248 (mt-10) REVERT: G 139 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5952 (ttm170) REVERT: G 148 LYS cc_start: 0.7505 (mttt) cc_final: 0.7237 (mtpm) REVERT: G 156 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7735 (mttt) REVERT: G 159 ARG cc_start: 0.8366 (mtt-85) cc_final: 0.7808 (mtm110) REVERT: G 166 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7129 (mt0) REVERT: G 198 LYS cc_start: 0.8272 (tttt) cc_final: 0.7497 (mptt) REVERT: H 19 GLU cc_start: 0.4252 (tp30) cc_final: 0.3975 (tp30) REVERT: H 36 LEU cc_start: 0.5523 (tt) cc_final: 0.4981 (pp) REVERT: H 90 MET cc_start: 0.7002 (tpp) cc_final: 0.6625 (tpt) REVERT: J 105 ARG cc_start: 0.4822 (mtt180) cc_final: 0.4449 (mmt-90) REVERT: J 109 LEU cc_start: 0.6222 (tp) cc_final: 0.5817 (mt) REVERT: J 115 LEU cc_start: 0.4498 (mm) cc_final: 0.4212 (mm) REVERT: J 121 LEU cc_start: 0.4517 (tp) cc_final: 0.4143 (mm) REVERT: J 173 ARG cc_start: 0.6589 (ttt-90) cc_final: 0.6162 (ttm-80) REVERT: L 74 GLN cc_start: 0.6639 (tp40) cc_final: 0.5916 (mm110) REVERT: L 76 ARG cc_start: 0.6816 (mtp85) cc_final: 0.6524 (mtt180) REVERT: L 84 ARG cc_start: 0.6254 (ttm-80) cc_final: 0.5878 (ttm170) REVERT: L 160 LYS cc_start: 0.7319 (mttp) cc_final: 0.6464 (mmtp) REVERT: L 162 GLN cc_start: 0.7539 (pt0) cc_final: 0.6608 (pt0) outliers start: 102 outliers final: 41 residues processed: 511 average time/residue: 1.8334 time to fit residues: 1058.8887 Evaluate side-chains 478 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 409 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 345 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 270 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 318 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN E 363 ASN E 364 ASN J 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.141663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.105068 restraints weight = 32597.959| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.43 r_work: 0.2907 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30023 Z= 0.155 Angle : 0.542 10.805 40670 Z= 0.279 Chirality : 0.044 0.179 4560 Planarity : 0.005 0.047 5330 Dihedral : 4.624 62.385 4185 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.14 % Rotamer: Outliers : 3.76 % Allowed : 16.74 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3764 helix: 1.85 (0.13), residues: 1570 sheet: -0.18 (0.21), residues: 590 loop : 0.30 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 119 HIS 0.003 0.001 HIS C 418 PHE 0.017 0.002 PHE C 559 TYR 0.015 0.002 TYR H 89 ARG 0.007 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 1332) hydrogen bonds : angle 4.56486 ( 3807) covalent geometry : bond 0.00371 (30023) covalent geometry : angle 0.54179 (40670) *********************** 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 533 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 417 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8397 (mttt) cc_final: 0.8085 (mmmt) REVERT: A 53 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: A 109 HIS cc_start: 0.7882 (m-70) cc_final: 0.7650 (m-70) REVERT: A 191 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7795 (ttp80) REVERT: A 340 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7285 (mpt-90) REVERT: A 445 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 449 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: A 498 ASN cc_start: 0.8835 (t0) cc_final: 0.8625 (t0) REVERT: A 571 GLN cc_start: 0.6615 (mm-40) cc_final: 0.6348 (tt0) REVERT: B 19 MET cc_start: 0.8850 (mmm) cc_final: 0.8342 (mmm) REVERT: B 32 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: B 93 ARG cc_start: 0.7836 (mmp80) cc_final: 0.7205 (mmm160) REVERT: B 96 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6654 (mt-10) REVERT: B 122 MET cc_start: 0.8112 (mtm) cc_final: 0.7855 (mtt) REVERT: B 124 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7005 (mppt) REVERT: B 130 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7106 (ptm-80) REVERT: B 154 ARG cc_start: 0.7119 (mtp-110) cc_final: 0.6872 (ptp90) REVERT: B 170 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7169 (mt-10) REVERT: B 391 MET cc_start: 0.7538 (mmp) cc_final: 0.7210 (mmt) REVERT: B 410 ASP cc_start: 0.8495 (p0) cc_final: 0.8193 (p0) REVERT: B 467 ILE cc_start: 0.7361 (mt) cc_final: 0.7045 (tp) REVERT: B 524 LYS cc_start: 0.7578 (mttp) cc_final: 0.7053 (mppt) REVERT: C 3 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7361 (tp40) REVERT: C 29 LYS cc_start: 0.8867 (mttp) cc_final: 0.8632 (mmtp) REVERT: C 156 ARG cc_start: 0.7370 (ttm-80) cc_final: 0.7015 (mmm-85) REVERT: C 180 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6792 (mm-30) REVERT: C 268 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: C 336 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: C 342 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: C 348 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: C 408 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8115 (ttt-90) REVERT: C 410 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8269 (t0) REVERT: C 547 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6867 (tpt90) REVERT: D 52 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: D 98 LYS cc_start: 0.7888 (tttt) cc_final: 0.7184 (mtpt) REVERT: D 128 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: D 162 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: D 236 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8375 (mtt90) REVERT: D 248 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7523 (mm-30) REVERT: D 280 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7844 (ttp-110) REVERT: D 373 GLU cc_start: 0.7594 (pm20) cc_final: 0.7296 (pm20) REVERT: D 398 ILE cc_start: 0.8265 (mt) cc_final: 0.7936 (mm) REVERT: D 413 GLN cc_start: 0.7967 (mt0) cc_final: 0.7715 (mt0) REVERT: D 420 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7435 (mmt-90) REVERT: D 450 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6678 (mm-30) REVERT: D 457 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6025 (m-30) REVERT: E 26 ASP cc_start: 0.7681 (m-30) cc_final: 0.7384 (m-30) REVERT: E 61 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: E 98 LYS cc_start: 0.8106 (mttt) cc_final: 0.7818 (mmtp) REVERT: E 200 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8172 (mt-10) REVERT: E 207 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: E 211 THR cc_start: 0.8492 (p) cc_final: 0.8258 (m) REVERT: E 216 ARG cc_start: 0.8331 (ptt90) cc_final: 0.7854 (ptt-90) REVERT: E 274 ARG cc_start: 0.7918 (mtp180) cc_final: 0.6872 (mmp-170) REVERT: E 388 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8194 (t0) REVERT: E 394 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8083 (mttp) REVERT: F 25 LYS cc_start: 0.7117 (ptmm) cc_final: 0.6834 (mtpt) REVERT: F 53 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7511 (mm-30) REVERT: F 79 VAL cc_start: 0.8763 (p) cc_final: 0.8459 (m) REVERT: F 98 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7822 (mmtp) REVERT: F 125 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7302 (ttm170) REVERT: F 265 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7813 (tm-30) REVERT: F 373 GLU cc_start: 0.7575 (mp0) cc_final: 0.7195 (pm20) REVERT: F 394 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7624 (mttt) REVERT: F 437 GLN cc_start: 0.8816 (tt0) cc_final: 0.8551 (tt0) REVERT: F 456 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7635 (mmmt) REVERT: G 38 GLU cc_start: 0.7918 (tt0) cc_final: 0.7601 (tp30) REVERT: G 47 MET cc_start: 0.7092 (tpp) cc_final: 0.6730 (tpp) REVERT: G 48 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6223 (mt-10) REVERT: G 139 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.5936 (ttm170) REVERT: G 148 LYS cc_start: 0.7521 (mttt) cc_final: 0.7238 (mtpm) REVERT: G 156 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7798 (mttt) REVERT: G 159 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.7767 (mtm110) REVERT: G 166 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: G 198 LYS cc_start: 0.8232 (tttt) cc_final: 0.7444 (mptt) REVERT: H 15 LEU cc_start: 0.5588 (tp) cc_final: 0.5289 (tp) REVERT: H 19 GLU cc_start: 0.4261 (tp30) cc_final: 0.4004 (tp30) REVERT: H 48 ASP cc_start: 0.5743 (OUTLIER) cc_final: 0.4675 (p0) REVERT: H 90 MET cc_start: 0.6950 (tpp) cc_final: 0.6370 (tpp) REVERT: J 105 ARG cc_start: 0.4740 (mtt180) cc_final: 0.4410 (mmt-90) REVERT: J 109 LEU cc_start: 0.6186 (tp) cc_final: 0.5808 (mt) REVERT: J 115 LEU cc_start: 0.4439 (mm) cc_final: 0.4156 (mm) REVERT: J 121 LEU cc_start: 0.4508 (tp) cc_final: 0.4080 (mm) REVERT: L 74 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.5859 (mm110) REVERT: L 76 ARG cc_start: 0.6814 (mtp85) cc_final: 0.6339 (mtt180) REVERT: L 84 ARG cc_start: 0.6252 (ttm-80) cc_final: 0.5836 (ttm170) REVERT: L 160 LYS cc_start: 0.7379 (mttp) cc_final: 0.6452 (mmtp) REVERT: L 162 GLN cc_start: 0.7585 (pt0) cc_final: 0.6692 (pt0) outliers start: 116 outliers final: 48 residues processed: 490 average time/residue: 1.8688 time to fit residues: 1037.4672 Evaluate side-chains 480 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 401 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 76 optimal weight: 0.5980 chunk 338 optimal weight: 9.9990 chunk 368 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN F 363 ASN F 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.140376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.103422 restraints weight = 32848.245| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.53 r_work: 0.2869 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30023 Z= 0.200 Angle : 0.595 10.250 40670 Z= 0.307 Chirality : 0.046 0.189 4560 Planarity : 0.005 0.053 5330 Dihedral : 4.869 64.900 4185 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.15 % Favored : 97.82 % Rotamer: Outliers : 4.18 % Allowed : 16.51 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3764 helix: 1.65 (0.13), residues: 1573 sheet: -0.24 (0.21), residues: 585 loop : 0.16 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 119 HIS 0.003 0.001 HIS C 418 PHE 0.026 0.002 PHE A 574 TYR 0.016 0.002 TYR H 89 ARG 0.008 0.001 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 1332) hydrogen bonds : angle 4.69736 ( 3807) covalent geometry : bond 0.00487 (30023) covalent geometry : angle 0.59478 (40670) *********************** 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 539 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 410 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8429 (mttt) cc_final: 0.8167 (mtpp) REVERT: A 53 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: A 109 HIS cc_start: 0.7889 (m-70) cc_final: 0.7538 (m170) REVERT: A 191 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7792 (ttp80) REVERT: A 340 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7404 (mpt-90) REVERT: A 445 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: A 449 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 469 GLN cc_start: 0.7506 (mt0) cc_final: 0.7019 (mm110) REVERT: A 498 ASN cc_start: 0.8870 (t0) cc_final: 0.8659 (t0) REVERT: A 571 GLN cc_start: 0.6631 (mm-40) cc_final: 0.6394 (tt0) REVERT: B 19 MET cc_start: 0.8865 (mmm) cc_final: 0.8278 (mmm) REVERT: B 32 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: B 93 ARG cc_start: 0.7848 (mmp80) cc_final: 0.7175 (mmm160) REVERT: B 122 MET cc_start: 0.8095 (mtm) cc_final: 0.7837 (mtt) REVERT: B 124 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6945 (mppt) REVERT: B 130 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7172 (ptm-80) REVERT: B 156 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6433 (tpp80) REVERT: B 391 MET cc_start: 0.7520 (mmp) cc_final: 0.7310 (mmt) REVERT: B 410 ASP cc_start: 0.8582 (p0) cc_final: 0.8231 (p0) REVERT: B 467 ILE cc_start: 0.7364 (mt) cc_final: 0.7065 (tp) REVERT: B 524 LYS cc_start: 0.7573 (mttp) cc_final: 0.7005 (mppt) REVERT: C 3 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: C 29 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8650 (mmtp) REVERT: C 129 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7482 (m) REVERT: C 156 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.7124 (mmm-85) REVERT: C 180 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6839 (mm-30) REVERT: C 191 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8143 (mtm180) REVERT: C 336 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7914 (tp30) REVERT: C 342 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 348 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: C 408 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8133 (ttt-90) REVERT: C 547 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6836 (tpt90) REVERT: D 52 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: D 98 LYS cc_start: 0.7879 (tttt) cc_final: 0.7222 (mtpt) REVERT: D 106 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7853 (pt) REVERT: D 128 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7319 (pp20) REVERT: D 162 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: D 236 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8413 (mtt90) REVERT: D 248 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7533 (mm-30) REVERT: D 280 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7848 (ttp-110) REVERT: D 398 ILE cc_start: 0.8266 (mt) cc_final: 0.7928 (mm) REVERT: D 413 GLN cc_start: 0.8000 (mt0) cc_final: 0.7790 (mt0) REVERT: D 420 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7436 (mmt-90) REVERT: D 450 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6734 (mm-30) REVERT: D 457 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6068 (m-30) REVERT: E 26 ASP cc_start: 0.7701 (m-30) cc_final: 0.7420 (m-30) REVERT: E 61 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6816 (pt0) REVERT: E 98 LYS cc_start: 0.8135 (mttt) cc_final: 0.7766 (mmtp) REVERT: E 200 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8162 (mt-10) REVERT: E 207 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: E 211 THR cc_start: 0.8508 (p) cc_final: 0.8246 (m) REVERT: E 216 ARG cc_start: 0.8382 (ptt90) cc_final: 0.7908 (ptt-90) REVERT: E 274 ARG cc_start: 0.7911 (mtp180) cc_final: 0.6845 (mmp-170) REVERT: E 376 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7325 (tmtm) REVERT: E 388 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8213 (t0) REVERT: E 394 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8088 (mttp) REVERT: E 452 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7629 (mmtp) REVERT: F 25 LYS cc_start: 0.7182 (ptmm) cc_final: 0.6894 (mtpt) REVERT: F 53 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7570 (mm-30) REVERT: F 79 VAL cc_start: 0.8740 (p) cc_final: 0.8289 (t) REVERT: F 98 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7836 (mmtp) REVERT: F 125 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7315 (ttm170) REVERT: F 210 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7810 (ttt-90) REVERT: F 265 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7887 (tm-30) REVERT: F 373 GLU cc_start: 0.7588 (mp0) cc_final: 0.7206 (pm20) REVERT: F 380 ASP cc_start: 0.8473 (m-30) cc_final: 0.8159 (m-30) REVERT: F 394 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7628 (mttt) REVERT: G 38 GLU cc_start: 0.8027 (tt0) cc_final: 0.7670 (tp30) REVERT: G 47 MET cc_start: 0.7100 (tpp) cc_final: 0.6741 (tpp) REVERT: G 48 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6280 (mt-10) REVERT: G 139 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5986 (ttm170) REVERT: G 148 LYS cc_start: 0.7593 (mttt) cc_final: 0.7274 (mtpm) REVERT: G 156 LYS cc_start: 0.8385 (mtpp) cc_final: 0.7858 (mttt) REVERT: G 159 ARG cc_start: 0.8388 (mtt-85) cc_final: 0.7801 (mtm110) REVERT: G 166 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7286 (mt0) REVERT: G 198 LYS cc_start: 0.8280 (tttt) cc_final: 0.7461 (mptt) REVERT: H 19 GLU cc_start: 0.4531 (tp30) cc_final: 0.4215 (tp30) REVERT: H 48 ASP cc_start: 0.5739 (OUTLIER) cc_final: 0.4652 (p0) REVERT: H 90 MET cc_start: 0.6972 (tpp) cc_final: 0.6598 (tpp) REVERT: J 105 ARG cc_start: 0.4757 (mtt180) cc_final: 0.4450 (mmt-90) REVERT: J 109 LEU cc_start: 0.6066 (tp) cc_final: 0.5766 (mt) REVERT: J 121 LEU cc_start: 0.4566 (tp) cc_final: 0.4030 (mm) REVERT: J 126 GLU cc_start: 0.4186 (OUTLIER) cc_final: 0.3806 (mp0) REVERT: L 74 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.5873 (mm110) REVERT: L 76 ARG cc_start: 0.6899 (mtp85) cc_final: 0.6609 (mtt180) REVERT: L 81 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6038 (tp30) REVERT: L 84 ARG cc_start: 0.6258 (ttm-80) cc_final: 0.5883 (ttm170) REVERT: L 145 GLU cc_start: 0.5345 (mt-10) cc_final: 0.5115 (tt0) REVERT: L 160 LYS cc_start: 0.7459 (mttp) cc_final: 0.6465 (mmtp) REVERT: L 162 GLN cc_start: 0.7770 (pt0) cc_final: 0.6808 (pt0) outliers start: 129 outliers final: 46 residues processed: 488 average time/residue: 1.8524 time to fit residues: 1021.3536 Evaluate side-chains 485 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 403 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 133 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 131 optimal weight: 0.1980 chunk 164 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 215 optimal weight: 0.6980 chunk 337 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN H 84 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.104427 restraints weight = 32657.653| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.44 r_work: 0.2890 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30023 Z= 0.174 Angle : 0.565 10.120 40670 Z= 0.292 Chirality : 0.045 0.191 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.794 64.813 4185 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.99 % Favored : 97.98 % Rotamer: Outliers : 3.99 % Allowed : 17.22 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1565 sheet: -0.34 (0.21), residues: 581 loop : 0.16 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 119 HIS 0.003 0.001 HIS A 185 PHE 0.025 0.002 PHE A 574 TYR 0.016 0.002 TYR H 89 ARG 0.008 0.001 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 1332) hydrogen bonds : angle 4.62886 ( 3807) covalent geometry : bond 0.00419 (30023) covalent geometry : angle 0.56487 (40670) *********************** 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 538 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 415 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8433 (mttt) cc_final: 0.8173 (mtpp) REVERT: A 53 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: A 109 HIS cc_start: 0.7866 (m-70) cc_final: 0.7525 (m170) REVERT: A 156 ARG cc_start: 0.6627 (ttp80) cc_final: 0.6287 (ttp80) REVERT: A 191 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7795 (ttp80) REVERT: A 340 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7334 (mpt-90) REVERT: A 445 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: A 449 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: A 469 GLN cc_start: 0.7456 (mt0) cc_final: 0.6985 (mm110) REVERT: A 498 ASN cc_start: 0.8863 (t0) cc_final: 0.8653 (t0) REVERT: A 571 GLN cc_start: 0.6563 (mm-40) cc_final: 0.6306 (tt0) REVERT: B 19 MET cc_start: 0.8848 (mmm) cc_final: 0.8157 (mmm) REVERT: B 32 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7078 (mm-30) REVERT: B 122 MET cc_start: 0.8108 (mtm) cc_final: 0.7863 (mtt) REVERT: B 124 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6941 (mppt) REVERT: B 130 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7121 (ptm-80) REVERT: B 156 ARG cc_start: 0.7244 (mtp85) cc_final: 0.6426 (tpp80) REVERT: B 410 ASP cc_start: 0.8563 (p0) cc_final: 0.8212 (p0) REVERT: B 467 ILE cc_start: 0.7291 (mt) cc_final: 0.6998 (tp) REVERT: B 509 MET cc_start: 0.8906 (mmm) cc_final: 0.8656 (mmm) REVERT: B 524 LYS cc_start: 0.7499 (mttp) cc_final: 0.6922 (mppt) REVERT: C 3 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: C 29 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8648 (mmtp) REVERT: C 129 VAL cc_start: 0.7994 (OUTLIER) cc_final: 0.7633 (p) REVERT: C 156 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.7098 (mmm-85) REVERT: C 180 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6758 (mm-30) REVERT: C 336 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: C 342 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: C 348 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: C 408 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8089 (ttt-90) REVERT: C 547 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6923 (tpt90) REVERT: D 52 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: D 98 LYS cc_start: 0.7893 (tttt) cc_final: 0.7410 (mmmm) REVERT: D 106 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7833 (pt) REVERT: D 128 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7322 (pp20) REVERT: D 162 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: D 236 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8403 (mtt90) REVERT: D 248 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7506 (mm-30) REVERT: D 280 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7864 (ttp-110) REVERT: D 398 ILE cc_start: 0.8291 (mt) cc_final: 0.7981 (mm) REVERT: D 413 GLN cc_start: 0.7992 (mt0) cc_final: 0.7732 (mt0) REVERT: D 420 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7403 (mmt-90) REVERT: D 457 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: E 26 ASP cc_start: 0.7693 (m-30) cc_final: 0.7406 (m-30) REVERT: E 61 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6830 (pt0) REVERT: E 98 LYS cc_start: 0.8125 (mttt) cc_final: 0.7788 (mmtp) REVERT: E 103 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7744 (mp) REVERT: E 200 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8154 (mt-10) REVERT: E 207 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: E 211 THR cc_start: 0.8488 (p) cc_final: 0.8249 (m) REVERT: E 216 ARG cc_start: 0.8363 (ptt90) cc_final: 0.7919 (ptt-90) REVERT: E 274 ARG cc_start: 0.7907 (mtp180) cc_final: 0.6869 (mmp-170) REVERT: E 376 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7350 (tmtm) REVERT: E 388 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8189 (t0) REVERT: E 394 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8053 (mttp) REVERT: E 452 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7604 (mmtp) REVERT: F 25 LYS cc_start: 0.7092 (ptmm) cc_final: 0.6843 (mtpt) REVERT: F 53 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7515 (mm-30) REVERT: F 79 VAL cc_start: 0.8761 (p) cc_final: 0.8274 (t) REVERT: F 98 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7799 (mmtp) REVERT: F 125 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7325 (ttm170) REVERT: F 210 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7789 (ttt-90) REVERT: F 265 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7873 (tm-30) REVERT: F 373 GLU cc_start: 0.7561 (mp0) cc_final: 0.7195 (pm20) REVERT: F 380 ASP cc_start: 0.8490 (m-30) cc_final: 0.8212 (m-30) REVERT: F 394 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7649 (mttt) REVERT: G 30 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8109 (mtpt) REVERT: G 38 GLU cc_start: 0.7973 (tt0) cc_final: 0.7619 (tp30) REVERT: G 47 MET cc_start: 0.7156 (tpp) cc_final: 0.6788 (tpp) REVERT: G 48 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6228 (mt-10) REVERT: G 139 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.5931 (ttm170) REVERT: G 148 LYS cc_start: 0.7562 (mttt) cc_final: 0.7269 (mtpm) REVERT: G 156 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7848 (mttt) REVERT: G 159 ARG cc_start: 0.8413 (mtt-85) cc_final: 0.7828 (mtm110) REVERT: G 166 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: G 198 LYS cc_start: 0.8288 (tttt) cc_final: 0.7482 (mptt) REVERT: H 15 LEU cc_start: 0.5555 (tp) cc_final: 0.5227 (tp) REVERT: H 48 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.4687 (p0) REVERT: H 90 MET cc_start: 0.7073 (tpp) cc_final: 0.6640 (tpp) REVERT: J 88 ARG cc_start: 0.5466 (ptm-80) cc_final: 0.5262 (ptm-80) REVERT: J 105 ARG cc_start: 0.4767 (mtt180) cc_final: 0.4408 (mmt-90) REVERT: J 109 LEU cc_start: 0.5906 (tp) cc_final: 0.5622 (mt) REVERT: J 126 GLU cc_start: 0.4280 (OUTLIER) cc_final: 0.3835 (mp0) REVERT: L 74 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.5877 (mm-40) REVERT: L 76 ARG cc_start: 0.6849 (mtp85) cc_final: 0.6560 (mtt180) REVERT: L 84 ARG cc_start: 0.6180 (ttm-80) cc_final: 0.5785 (ttm170) REVERT: L 145 GLU cc_start: 0.5273 (mt-10) cc_final: 0.4941 (tt0) REVERT: L 160 LYS cc_start: 0.7494 (mttp) cc_final: 0.6642 (mmtm) REVERT: L 162 GLN cc_start: 0.7707 (pt0) cc_final: 0.6770 (pt0) outliers start: 123 outliers final: 55 residues processed: 493 average time/residue: 1.8503 time to fit residues: 1034.5884 Evaluate side-chains 493 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 401 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN F 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.140194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.103701 restraints weight = 32834.341| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.51 r_work: 0.2858 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30023 Z= 0.206 Angle : 0.604 10.895 40670 Z= 0.312 Chirality : 0.046 0.193 4560 Planarity : 0.005 0.054 5330 Dihedral : 4.928 66.172 4185 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 3.96 % Allowed : 17.32 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3764 helix: 1.60 (0.13), residues: 1565 sheet: -0.28 (0.21), residues: 581 loop : 0.09 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 119 HIS 0.003 0.001 HIS C 418 PHE 0.024 0.002 PHE A 574 TYR 0.018 0.002 TYR H 21 ARG 0.008 0.001 ARG L 88 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 1332) hydrogen bonds : angle 4.71221 ( 3807) covalent geometry : bond 0.00501 (30023) covalent geometry : angle 0.60389 (40670) *********************** 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 523 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 401 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8424 (mttt) cc_final: 0.8171 (mtpp) REVERT: A 53 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: A 109 HIS cc_start: 0.7869 (m-70) cc_final: 0.7542 (m170) REVERT: A 156 ARG cc_start: 0.6643 (ttp80) cc_final: 0.6299 (ttp80) REVERT: A 191 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7811 (ttp80) REVERT: A 340 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7398 (mpt-90) REVERT: A 391 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7953 (mpp) REVERT: A 445 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: A 449 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: A 469 GLN cc_start: 0.7525 (mt0) cc_final: 0.7030 (mm110) REVERT: A 541 GLN cc_start: 0.6839 (mt0) cc_final: 0.6612 (mm-40) REVERT: A 546 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: A 571 GLN cc_start: 0.6652 (mm-40) cc_final: 0.6426 (tt0) REVERT: B 19 MET cc_start: 0.8848 (mmm) cc_final: 0.8157 (mmm) REVERT: B 32 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: B 122 MET cc_start: 0.8143 (mtm) cc_final: 0.7896 (mtt) REVERT: B 124 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6910 (mppt) REVERT: B 130 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7188 (ptm-80) REVERT: B 410 ASP cc_start: 0.8595 (p0) cc_final: 0.8295 (p0) REVERT: B 467 ILE cc_start: 0.7432 (mt) cc_final: 0.7154 (tp) REVERT: B 524 LYS cc_start: 0.7548 (mttp) cc_final: 0.6983 (mppt) REVERT: C 29 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8708 (mmtp) REVERT: C 156 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7137 (mmm-85) REVERT: C 180 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6755 (mm-30) REVERT: C 191 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8188 (mtm180) REVERT: C 336 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7966 (tp30) REVERT: C 342 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: C 408 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8171 (ttt-90) REVERT: C 547 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6895 (tpt90) REVERT: D 52 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: D 98 LYS cc_start: 0.7936 (tttt) cc_final: 0.7426 (mmmm) REVERT: D 106 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7835 (pt) REVERT: D 128 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7393 (pp20) REVERT: D 162 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: D 236 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (mtt90) REVERT: D 248 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7580 (mm-30) REVERT: D 280 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7860 (ttp-110) REVERT: D 398 ILE cc_start: 0.8271 (mt) cc_final: 0.7947 (mm) REVERT: D 413 GLN cc_start: 0.8042 (mt0) cc_final: 0.7779 (mt0) REVERT: D 420 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7452 (mmt-90) REVERT: D 457 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6119 (m-30) REVERT: E 26 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: E 36 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8020 (tttp) REVERT: E 61 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6885 (pt0) REVERT: E 98 LYS cc_start: 0.8112 (mttt) cc_final: 0.7773 (mmtp) REVERT: E 103 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7867 (mp) REVERT: E 200 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8200 (mt-10) REVERT: E 207 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: E 211 THR cc_start: 0.8543 (p) cc_final: 0.8295 (m) REVERT: E 216 ARG cc_start: 0.8402 (ptt90) cc_final: 0.7957 (ptt-90) REVERT: E 274 ARG cc_start: 0.7956 (mtp180) cc_final: 0.6876 (mmp-170) REVERT: E 376 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7435 (tmtm) REVERT: E 388 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8233 (t0) REVERT: E 452 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7636 (mmtp) REVERT: F 25 LYS cc_start: 0.7097 (ptmm) cc_final: 0.6828 (mtpt) REVERT: F 53 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7587 (mm-30) REVERT: F 79 VAL cc_start: 0.8758 (p) cc_final: 0.8262 (t) REVERT: F 98 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7871 (mmtp) REVERT: F 125 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7324 (ttm170) REVERT: F 210 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7829 (ttt-90) REVERT: F 265 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7903 (tm-30) REVERT: F 373 GLU cc_start: 0.7629 (mp0) cc_final: 0.7238 (pm20) REVERT: F 380 ASP cc_start: 0.8517 (m-30) cc_final: 0.8206 (m-30) REVERT: F 394 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7659 (mttt) REVERT: G 30 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8163 (mtpt) REVERT: G 38 GLU cc_start: 0.8041 (tt0) cc_final: 0.7686 (tp30) REVERT: G 47 MET cc_start: 0.7196 (tpp) cc_final: 0.6823 (tpp) REVERT: G 48 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6212 (mt-10) REVERT: G 139 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.5949 (ttm170) REVERT: G 148 LYS cc_start: 0.7608 (mttt) cc_final: 0.7321 (mtpm) REVERT: G 156 LYS cc_start: 0.8453 (mtpp) cc_final: 0.7913 (mttt) REVERT: G 159 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.7842 (mtm110) REVERT: G 166 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7215 (mt0) REVERT: G 198 LYS cc_start: 0.8315 (tttt) cc_final: 0.7491 (mptt) REVERT: H 15 LEU cc_start: 0.5544 (tp) cc_final: 0.5217 (tp) REVERT: H 48 ASP cc_start: 0.5751 (OUTLIER) cc_final: 0.4667 (p0) REVERT: H 90 MET cc_start: 0.7080 (tpp) cc_final: 0.6661 (tpp) REVERT: J 105 ARG cc_start: 0.4766 (mtt180) cc_final: 0.4413 (mmt-90) REVERT: J 109 LEU cc_start: 0.5879 (tp) cc_final: 0.5590 (mt) REVERT: J 121 LEU cc_start: 0.4632 (tp) cc_final: 0.4227 (mp) REVERT: J 126 GLU cc_start: 0.4214 (OUTLIER) cc_final: 0.3718 (mp0) REVERT: L 74 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.5864 (mm-40) REVERT: L 76 ARG cc_start: 0.6913 (mtp85) cc_final: 0.6616 (mtt180) REVERT: L 81 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6044 (tp30) REVERT: L 84 ARG cc_start: 0.6192 (ttm-80) cc_final: 0.5889 (ttm170) REVERT: L 145 GLU cc_start: 0.5206 (mt-10) cc_final: 0.4798 (tt0) REVERT: L 160 LYS cc_start: 0.7513 (mttp) cc_final: 0.6644 (mmtm) REVERT: L 162 GLN cc_start: 0.7728 (pt0) cc_final: 0.6784 (pt0) REVERT: L 167 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5483 (mp) outliers start: 122 outliers final: 60 residues processed: 479 average time/residue: 1.8634 time to fit residues: 1007.6399 Evaluate side-chains 493 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 394 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 342 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 240 optimal weight: 0.0980 chunk 330 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 304 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN C 3 GLN C 541 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.141410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.104871 restraints weight = 32769.699| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.43 r_work: 0.2900 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30023 Z= 0.145 Angle : 0.547 11.837 40670 Z= 0.282 Chirality : 0.044 0.190 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.729 65.853 4185 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.17 % Rotamer: Outliers : 3.37 % Allowed : 18.20 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3764 helix: 1.77 (0.13), residues: 1565 sheet: -0.30 (0.21), residues: 581 loop : 0.17 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 119 HIS 0.003 0.001 HIS A 185 PHE 0.024 0.002 PHE E 130 TYR 0.017 0.001 TYR H 89 ARG 0.010 0.000 ARG L 88 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 1332) hydrogen bonds : angle 4.57519 ( 3807) covalent geometry : bond 0.00344 (30023) covalent geometry : angle 0.54693 (40670) *********************** 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 509 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 405 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8407 (mttt) cc_final: 0.8150 (mtpp) REVERT: A 53 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: A 109 HIS cc_start: 0.7802 (m-70) cc_final: 0.7476 (m170) REVERT: A 156 ARG cc_start: 0.6618 (ttp80) cc_final: 0.6277 (ttp80) REVERT: A 191 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7806 (ttp80) REVERT: A 340 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7296 (mpt-90) REVERT: A 445 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: A 449 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 498 ASN cc_start: 0.8841 (t0) cc_final: 0.8627 (t0) REVERT: A 546 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: A 571 GLN cc_start: 0.6537 (mm-40) cc_final: 0.6291 (tt0) REVERT: B 19 MET cc_start: 0.8837 (mmm) cc_final: 0.8155 (mmm) REVERT: B 32 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: B 96 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6699 (mt-10) REVERT: B 116 LYS cc_start: 0.8050 (mttp) cc_final: 0.7593 (mmtp) REVERT: B 122 MET cc_start: 0.8082 (mtm) cc_final: 0.7863 (mtt) REVERT: B 124 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6990 (mppt) REVERT: B 130 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7122 (ptm-80) REVERT: B 156 ARG cc_start: 0.7181 (mtp85) cc_final: 0.6408 (tpp80) REVERT: B 276 LYS cc_start: 0.7337 (mtmt) cc_final: 0.6587 (ptmt) REVERT: B 410 ASP cc_start: 0.8556 (p0) cc_final: 0.8259 (p0) REVERT: B 467 ILE cc_start: 0.7385 (mt) cc_final: 0.7122 (tp) REVERT: B 524 LYS cc_start: 0.7524 (mttp) cc_final: 0.6988 (mppt) REVERT: C 29 LYS cc_start: 0.8880 (mttp) cc_final: 0.8634 (mmtp) REVERT: C 129 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7434 (m) REVERT: C 156 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.7103 (mmm-85) REVERT: C 180 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6738 (mm-30) REVERT: C 191 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8171 (mtm180) REVERT: C 336 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: C 342 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: C 547 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6880 (tpt90) REVERT: D 98 LYS cc_start: 0.7875 (tttt) cc_final: 0.7388 (mmmt) REVERT: D 106 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7834 (pt) REVERT: D 128 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: D 162 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: D 236 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8374 (mtt90) REVERT: D 248 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7530 (mm-30) REVERT: D 280 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7857 (ttp-110) REVERT: D 398 ILE cc_start: 0.8294 (mt) cc_final: 0.8004 (mm) REVERT: D 413 GLN cc_start: 0.8009 (mt0) cc_final: 0.7780 (mt0) REVERT: D 420 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7399 (mmt-90) REVERT: D 457 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6088 (m-30) REVERT: E 26 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: E 61 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6839 (pt0) REVERT: E 98 LYS cc_start: 0.8068 (mttt) cc_final: 0.7739 (mmtp) REVERT: E 103 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7840 (mp) REVERT: E 200 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8160 (mt-10) REVERT: E 207 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: E 211 THR cc_start: 0.8442 (p) cc_final: 0.8221 (m) REVERT: E 216 ARG cc_start: 0.8384 (ptt90) cc_final: 0.7947 (ptt-90) REVERT: E 274 ARG cc_start: 0.7895 (mtp180) cc_final: 0.6879 (mmp-170) REVERT: E 376 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7360 (tmtm) REVERT: E 388 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8180 (t0) REVERT: E 394 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8073 (mttp) REVERT: E 452 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7594 (mmtp) REVERT: F 25 LYS cc_start: 0.7078 (ptmm) cc_final: 0.6836 (mtpt) REVERT: F 53 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7518 (mm-30) REVERT: F 79 VAL cc_start: 0.8769 (p) cc_final: 0.8266 (t) REVERT: F 98 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7815 (mmtp) REVERT: F 125 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7300 (ttm170) REVERT: F 210 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7798 (ttt-90) REVERT: F 265 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7866 (tm-30) REVERT: F 373 GLU cc_start: 0.7566 (mp0) cc_final: 0.7194 (pm20) REVERT: F 380 ASP cc_start: 0.8492 (m-30) cc_final: 0.8229 (m-30) REVERT: F 394 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7638 (mttt) REVERT: G 38 GLU cc_start: 0.7962 (tt0) cc_final: 0.7626 (tp30) REVERT: G 47 MET cc_start: 0.7138 (tpp) cc_final: 0.6816 (tpp) REVERT: G 48 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6226 (mt-10) REVERT: G 139 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5846 (ttm170) REVERT: G 148 LYS cc_start: 0.7578 (mttt) cc_final: 0.7305 (mtpm) REVERT: G 156 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7836 (mttt) REVERT: G 159 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.7798 (mtm110) REVERT: G 166 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7092 (mt0) REVERT: G 198 LYS cc_start: 0.8268 (tttt) cc_final: 0.7459 (mptt) REVERT: H 15 LEU cc_start: 0.5513 (tp) cc_final: 0.5188 (tp) REVERT: H 48 ASP cc_start: 0.5696 (OUTLIER) cc_final: 0.4582 (p0) REVERT: H 90 MET cc_start: 0.7093 (tpp) cc_final: 0.6685 (tpp) REVERT: I 107 LEU cc_start: 0.5187 (OUTLIER) cc_final: 0.4931 (tp) REVERT: J 105 ARG cc_start: 0.4862 (mtt180) cc_final: 0.4478 (mmt-90) REVERT: J 109 LEU cc_start: 0.5879 (tp) cc_final: 0.5607 (mt) REVERT: J 121 LEU cc_start: 0.4540 (tp) cc_final: 0.4209 (mp) REVERT: J 126 GLU cc_start: 0.4271 (OUTLIER) cc_final: 0.3757 (mp0) REVERT: L 61 GLU cc_start: 0.3567 (OUTLIER) cc_final: 0.2695 (pt0) REVERT: L 74 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.5812 (mm-40) REVERT: L 76 ARG cc_start: 0.6885 (mtp85) cc_final: 0.6588 (mtt180) REVERT: L 81 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6086 (tp30) REVERT: L 84 ARG cc_start: 0.6201 (ttm-80) cc_final: 0.5817 (ttm170) REVERT: L 145 GLU cc_start: 0.5187 (mt-10) cc_final: 0.4761 (tt0) REVERT: L 160 LYS cc_start: 0.7480 (mttp) cc_final: 0.6627 (mmtm) REVERT: L 162 GLN cc_start: 0.7682 (pt0) cc_final: 0.6735 (pt0) outliers start: 104 outliers final: 57 residues processed: 473 average time/residue: 1.9067 time to fit residues: 1037.7518 Evaluate side-chains 485 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 392 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 233 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 369 optimal weight: 0.0020 chunk 280 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 397 GLN C 3 GLN E 129 GLN E 364 ASN F 166 GLN F 170 GLN F 363 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.141855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.103180 restraints weight = 32909.926| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.72 r_work: 0.2909 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30023 Z= 0.134 Angle : 0.532 12.231 40670 Z= 0.274 Chirality : 0.044 0.184 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.593 65.949 4185 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 3.21 % Allowed : 18.49 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.14), residues: 3764 helix: 1.82 (0.13), residues: 1575 sheet: -0.26 (0.21), residues: 597 loop : 0.25 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS A 185 PHE 0.019 0.002 PHE A 574 TYR 0.014 0.001 TYR H 89 ARG 0.012 0.000 ARG L 88 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 1332) hydrogen bonds : angle 4.49908 ( 3807) covalent geometry : bond 0.00316 (30023) covalent geometry : angle 0.53233 (40670) ********************** 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 503 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 404 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8364 (mttt) cc_final: 0.8077 (mtpp) REVERT: A 53 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7315 (mt-10) REVERT: A 109 HIS cc_start: 0.7818 (m-70) cc_final: 0.7500 (m170) REVERT: A 156 ARG cc_start: 0.6563 (ttp80) cc_final: 0.6208 (ttp80) REVERT: A 191 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7777 (ttp80) REVERT: A 340 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7297 (mpt-90) REVERT: A 445 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: A 449 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: A 546 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: A 571 GLN cc_start: 0.6435 (mm-40) cc_final: 0.6167 (tt0) REVERT: B 19 MET cc_start: 0.8791 (mmm) cc_final: 0.8219 (mmm) REVERT: B 32 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: B 96 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6658 (mt-10) REVERT: B 116 LYS cc_start: 0.7981 (mttp) cc_final: 0.7582 (mmtt) REVERT: B 122 MET cc_start: 0.8028 (mtm) cc_final: 0.7778 (mtt) REVERT: B 124 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6975 (mppt) REVERT: B 130 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7038 (ptm-80) REVERT: B 156 ARG cc_start: 0.7105 (mtp85) cc_final: 0.6295 (tpp80) REVERT: B 276 LYS cc_start: 0.7372 (mtmt) cc_final: 0.6565 (ptmt) REVERT: B 410 ASP cc_start: 0.8565 (p0) cc_final: 0.8239 (p0) REVERT: B 467 ILE cc_start: 0.7212 (mt) cc_final: 0.6958 (tp) REVERT: B 524 LYS cc_start: 0.7447 (mttp) cc_final: 0.6866 (mppt) REVERT: C 29 LYS cc_start: 0.8870 (mttp) cc_final: 0.8608 (mmtp) REVERT: C 156 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.7017 (mmm-85) REVERT: C 180 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6717 (mm-30) REVERT: C 191 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8108 (mtm180) REVERT: C 336 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: C 342 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: C 547 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6753 (tpt90) REVERT: D 62 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5860 (mt-10) REVERT: D 98 LYS cc_start: 0.7799 (tttt) cc_final: 0.7259 (mmmt) REVERT: D 106 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7803 (pt) REVERT: D 128 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: D 162 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: D 236 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (mtt90) REVERT: D 248 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7549 (mm-30) REVERT: D 280 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7817 (ttp-110) REVERT: D 398 ILE cc_start: 0.8281 (mt) cc_final: 0.8004 (mm) REVERT: D 413 GLN cc_start: 0.7981 (mt0) cc_final: 0.7748 (mt0) REVERT: D 420 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7429 (mmt-90) REVERT: D 457 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6101 (m-30) REVERT: E 26 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: E 61 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: E 98 LYS cc_start: 0.8078 (mttt) cc_final: 0.7696 (mmtp) REVERT: E 103 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7729 (mp) REVERT: E 200 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8133 (mt-10) REVERT: E 207 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: E 216 ARG cc_start: 0.8333 (ptt90) cc_final: 0.7887 (ptt-90) REVERT: E 274 ARG cc_start: 0.7889 (mtp180) cc_final: 0.6783 (mmp-170) REVERT: E 376 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7240 (tmtm) REVERT: E 388 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8222 (t0) REVERT: E 394 LYS cc_start: 0.8598 (mtmt) cc_final: 0.7995 (mttp) REVERT: E 452 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7571 (mmtp) REVERT: F 25 LYS cc_start: 0.7041 (ptmm) cc_final: 0.6785 (mtpt) REVERT: F 53 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7456 (mm-30) REVERT: F 79 VAL cc_start: 0.8720 (p) cc_final: 0.8221 (t) REVERT: F 98 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7708 (mmtp) REVERT: F 125 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7208 (ttm170) REVERT: F 210 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7767 (ttt-90) REVERT: F 265 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7791 (tm-30) REVERT: F 373 GLU cc_start: 0.7529 (mp0) cc_final: 0.7133 (pm20) REVERT: F 380 ASP cc_start: 0.8535 (m-30) cc_final: 0.8321 (m-30) REVERT: F 394 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7526 (mttt) REVERT: G 38 GLU cc_start: 0.7896 (tt0) cc_final: 0.7548 (tp30) REVERT: G 48 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6168 (mt-10) REVERT: G 139 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.5768 (ttm170) REVERT: G 148 LYS cc_start: 0.7509 (mttt) cc_final: 0.7046 (mtpt) REVERT: G 156 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7738 (mttt) REVERT: G 159 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.7717 (mtm110) REVERT: G 166 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7092 (mt0) REVERT: G 181 GLN cc_start: 0.8527 (mm110) cc_final: 0.8166 (mm-40) REVERT: G 198 LYS cc_start: 0.8240 (tttt) cc_final: 0.7372 (mptt) REVERT: H 48 ASP cc_start: 0.5627 (OUTLIER) cc_final: 0.4527 (p0) REVERT: H 90 MET cc_start: 0.6962 (tpp) cc_final: 0.6674 (tpp) REVERT: J 105 ARG cc_start: 0.4776 (mtt180) cc_final: 0.4385 (mmt-90) REVERT: J 109 LEU cc_start: 0.5766 (tp) cc_final: 0.5499 (mt) REVERT: J 121 LEU cc_start: 0.4552 (tp) cc_final: 0.4185 (mp) REVERT: L 61 GLU cc_start: 0.3378 (OUTLIER) cc_final: 0.2526 (pt0) REVERT: L 74 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.5771 (mm110) REVERT: L 76 ARG cc_start: 0.6814 (mtp85) cc_final: 0.6511 (mtt180) REVERT: L 81 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6028 (tp30) REVERT: L 84 ARG cc_start: 0.6103 (ttm-80) cc_final: 0.5761 (ttm170) REVERT: L 145 GLU cc_start: 0.5335 (mt-10) cc_final: 0.4851 (tt0) REVERT: L 160 LYS cc_start: 0.7464 (mttp) cc_final: 0.6560 (mmtm) REVERT: L 162 GLN cc_start: 0.7582 (pt0) cc_final: 0.6641 (pt0) outliers start: 99 outliers final: 54 residues processed: 470 average time/residue: 1.8449 time to fit residues: 980.8565 Evaluate side-chains 483 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 395 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 302 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 327 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 397 GLN C 541 GLN E 129 GLN E 413 GLN F 166 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.140878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.103916 restraints weight = 32641.711| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.50 r_work: 0.2867 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30023 Z= 0.171 Angle : 0.574 12.185 40670 Z= 0.295 Chirality : 0.045 0.188 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.743 66.255 4185 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.94 % Favored : 98.03 % Rotamer: Outliers : 3.31 % Allowed : 18.55 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3764 helix: 1.73 (0.13), residues: 1566 sheet: -0.23 (0.21), residues: 588 loop : 0.16 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS C 418 PHE 0.020 0.002 PHE A 574 TYR 0.015 0.002 TYR H 89 ARG 0.013 0.001 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 1332) hydrogen bonds : angle 4.59385 ( 3807) covalent geometry : bond 0.00412 (30023) covalent geometry : angle 0.57440 (40670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26993.92 seconds wall clock time: 463 minutes 55.68 seconds (27835.68 seconds total)