Starting phenix.real_space_refine on Mon Aug 25 15:22:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gxy_34365/08_2025/8gxy_34365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gxy_34365/08_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_34365/08_2025/8gxy_34365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gxy_34365/08_2025/8gxy_34365.map" model { file = "/net/cci-nas-00/data/ceres_data/8gxy_34365/08_2025/8gxy_34365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gxy_34365/08_2025/8gxy_34365.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.29, per 1000 atoms: 0.21 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.05 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: 5.46 Time building geometry restraints manager: 3.23 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: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.510 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- 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 : 5.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (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 ARG 0.005 0.000 ARG B 547 TYR 0.019 0.001 TYR D 331 PHE 0.014 0.002 PHE B 563 TRP 0.011 0.001 TRP A 119 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00498 (30023) covalent geometry : angle 0.51956 (40670) hydrogen bonds : bond 0.14095 ( 1332) hydrogen bonds : angle 6.05019 ( 3807) *********************** 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 : 0.753 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: 0.8941 time to fit residues: 835.2469 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 : 0.787 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- 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 283 HIS 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.144267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.107292 restraints weight = 32592.596| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.53 r_work: 0.2944 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30023 Z= 0.162 Angle : 0.566 10.463 40670 Z= 0.294 Chirality : 0.045 0.163 4560 Planarity : 0.005 0.064 5330 Dihedral : 4.618 60.947 4185 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.78 % Favored : 98.19 % Rotamer: Outliers : 3.28 % Allowed : 13.92 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.14), residues: 3764 helix: 1.77 (0.14), residues: 1583 sheet: -0.18 (0.22), residues: 577 loop : 0.26 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.016 0.002 TYR F 349 PHE 0.018 0.002 PHE E 414 TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00384 (30023) covalent geometry : angle 0.56634 (40670) hydrogen bonds : bond 0.05131 ( 1332) hydrogen bonds : angle 4.83905 ( 3807) *********************** 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 601 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 500 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8399 (mttt) cc_final: 0.8164 (mmmt) REVERT: A 53 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: A 109 HIS cc_start: 0.7985 (m-70) cc_final: 0.7719 (m-70) REVERT: A 169 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7342 (tp30) REVERT: A 191 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7835 (ttp80) REVERT: A 323 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8656 (mpp) REVERT: A 340 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7280 (mpt-90) REVERT: A 445 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 449 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: A 498 ASN cc_start: 0.8896 (t0) cc_final: 0.8668 (t0) REVERT: A 536 ILE cc_start: 0.7266 (tt) cc_final: 0.6689 (pp) REVERT: A 571 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6522 (tt0) REVERT: B 19 MET cc_start: 0.8807 (mmm) cc_final: 0.8599 (mmm) REVERT: B 32 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: B 93 ARG cc_start: 0.7731 (mtp180) cc_final: 0.7496 (mmp80) REVERT: B 122 MET cc_start: 0.8273 (mtm) cc_final: 0.8007 (mtt) REVERT: B 130 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7149 (ptm-80) REVERT: B 154 ARG cc_start: 0.7095 (mtp-110) cc_final: 0.6833 (ptp90) REVERT: B 158 LYS cc_start: 0.7671 (tttt) cc_final: 0.7253 (tttt) REVERT: B 325 ASP cc_start: 0.7503 (t0) cc_final: 0.7276 (t70) REVERT: B 391 MET cc_start: 0.7420 (mmp) cc_final: 0.7088 (mmt) REVERT: B 441 GLU cc_start: 0.7688 (tp30) cc_final: 0.7460 (mt-10) REVERT: B 474 ASP cc_start: 0.6887 (m-30) cc_final: 0.5970 (t0) REVERT: B 524 LYS cc_start: 0.7767 (tttt) cc_final: 0.7508 (mttp) REVERT: C 29 LYS cc_start: 0.8909 (mttp) cc_final: 0.8631 (mptt) REVERT: C 112 ASP cc_start: 0.8231 (t0) cc_final: 0.7951 (t0) REVERT: C 170 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6932 (tm-30) REVERT: C 180 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6869 (mm-30) REVERT: C 191 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8226 (mtm180) REVERT: C 268 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7225 (tt0) REVERT: C 342 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: C 547 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7333 (tpp80) REVERT: D 98 LYS cc_start: 0.7866 (tttt) cc_final: 0.7411 (mmtp) REVERT: D 162 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: D 236 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8422 (mtt90) REVERT: D 248 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7611 (mm-30) REVERT: D 280 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7947 (ttp-110) REVERT: D 305 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8093 (mttp) REVERT: D 398 ILE cc_start: 0.8129 (mt) cc_final: 0.7713 (mm) REVERT: D 413 GLN cc_start: 0.8010 (mt0) cc_final: 0.7797 (mt0) REVERT: D 450 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6679 (mm-30) REVERT: D 453 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.7854 (mtt90) REVERT: D 457 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6169 (m-30) REVERT: E 26 ASP cc_start: 0.7515 (m-30) cc_final: 0.7295 (m-30) REVERT: E 61 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6861 (pt0) REVERT: E 200 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8146 (mt-10) REVERT: E 216 ARG cc_start: 0.8260 (ptt90) cc_final: 0.7875 (ptt-90) REVERT: E 274 ARG cc_start: 0.7977 (mtp180) cc_final: 0.6783 (mmp-170) REVERT: E 368 LYS cc_start: 0.7494 (mtpt) cc_final: 0.7123 (mtmm) REVERT: E 388 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8240 (t0) REVERT: E 394 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8133 (mttp) REVERT: F 6 LYS cc_start: 0.7752 (tttt) cc_final: 0.7034 (pttt) REVERT: F 25 LYS cc_start: 0.7155 (ptmm) cc_final: 0.6840 (mtpt) REVERT: F 53 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7449 (mm-30) REVERT: F 79 VAL cc_start: 0.8770 (p) cc_final: 0.8441 (m) REVERT: F 81 ARG cc_start: 0.8622 (mtt90) cc_final: 0.8356 (mmt90) REVERT: F 98 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8043 (mmtp) REVERT: F 210 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7682 (ttt-90) REVERT: F 265 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7667 (tm-30) REVERT: F 437 GLN cc_start: 0.8772 (tt0) cc_final: 0.8367 (tt0) REVERT: F 465 GLN cc_start: 0.7661 (tt0) cc_final: 0.7397 (tt0) REVERT: G 38 GLU cc_start: 0.7849 (tt0) cc_final: 0.7562 (tp30) REVERT: G 47 MET cc_start: 0.7049 (tpp) cc_final: 0.6711 (mpp) REVERT: G 48 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6377 (mt-10) REVERT: G 139 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.5927 (ttm170) REVERT: G 148 LYS cc_start: 0.7436 (mttt) cc_final: 0.7055 (mtpt) REVERT: G 156 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7710 (mttt) REVERT: G 159 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.7869 (mtm110) REVERT: G 166 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7098 (mt0) REVERT: G 198 LYS cc_start: 0.8196 (tttt) cc_final: 0.7568 (mmtt) REVERT: H 36 LEU cc_start: 0.5372 (tt) cc_final: 0.4963 (pp) REVERT: H 90 MET cc_start: 0.6817 (tpp) cc_final: 0.6583 (tpp) REVERT: J 72 ARG cc_start: 0.4568 (ttp-110) cc_final: 0.4170 (mtt180) REVERT: J 105 ARG cc_start: 0.4932 (mtt180) cc_final: 0.4491 (mmt-90) REVERT: J 109 LEU cc_start: 0.6147 (tp) cc_final: 0.5864 (mt) REVERT: J 121 LEU cc_start: 0.4668 (tp) cc_final: 0.4310 (mm) REVERT: L 74 GLN cc_start: 0.6802 (tp40) cc_final: 0.6238 (tp40) REVERT: L 76 ARG cc_start: 0.6899 (mtp85) cc_final: 0.6677 (mtp180) REVERT: L 84 ARG cc_start: 0.6222 (ttm-80) cc_final: 0.5799 (ttm170) REVERT: L 153 ARG cc_start: 0.5770 (ttm170) cc_final: 0.5523 (ttp80) REVERT: L 160 LYS cc_start: 0.7366 (mttp) cc_final: 0.6422 (mmtp) REVERT: L 162 GLN cc_start: 0.7634 (pt0) cc_final: 0.6603 (pt0) outliers start: 101 outliers final: 33 residues processed: 562 average time/residue: 0.9811 time to fit residues: 620.4491 Evaluate side-chains 485 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 435 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 A residue 534 VAL 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 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 245 SER 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 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 280 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 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 173 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 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 = 0.3518 r_free = 0.3518 target = 0.142198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.104886 restraints weight = 32752.040| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.51 r_work: 0.2902 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2773 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= 0.169 Angle : 0.568 10.104 40670 Z= 0.293 Chirality : 0.045 0.165 4560 Planarity : 0.005 0.047 5330 Dihedral : 4.696 59.959 4185 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.25 % Rotamer: Outliers : 4.22 % Allowed : 14.53 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.14), residues: 3764 helix: 1.77 (0.13), residues: 1576 sheet: -0.13 (0.22), residues: 572 loop : 0.25 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 156 TYR 0.016 0.002 TYR B 523 PHE 0.019 0.002 PHE E 414 TRP 0.017 0.002 TRP B 119 HIS 0.004 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00407 (30023) covalent geometry : angle 0.56771 (40670) hydrogen bonds : bond 0.04927 ( 1332) hydrogen bonds : angle 4.68346 ( 3807) *********************** 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 583 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 453 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8408 (mttt) cc_final: 0.8089 (mmmt) REVERT: A 53 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: A 109 HIS cc_start: 0.7899 (m-70) cc_final: 0.7650 (m-70) REVERT: A 115 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8106 (tttp) REVERT: A 340 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7319 (mpt-90) REVERT: A 445 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: A 449 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: A 498 ASN cc_start: 0.8852 (t0) cc_final: 0.8626 (t0) REVERT: A 571 GLN cc_start: 0.6636 (mm-40) cc_final: 0.6345 (tt0) REVERT: B 19 MET cc_start: 0.8826 (mmm) cc_final: 0.8449 (mmm) REVERT: B 32 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: B 93 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7249 (mmm160) REVERT: B 122 MET cc_start: 0.8225 (mtm) cc_final: 0.7973 (mtt) REVERT: B 124 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7083 (mppt) REVERT: B 130 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7088 (ptm-80) REVERT: B 154 ARG cc_start: 0.7100 (mtp-110) cc_final: 0.6855 (ptp90) REVERT: B 156 ARG cc_start: 0.7184 (mtp85) cc_final: 0.6371 (tpp80) REVERT: B 158 LYS cc_start: 0.7622 (tttt) cc_final: 0.7142 (tttt) REVERT: B 276 LYS cc_start: 0.7422 (mmtt) cc_final: 0.7208 (mtmt) REVERT: B 391 MET cc_start: 0.7479 (mmp) cc_final: 0.7222 (mmt) REVERT: B 410 ASP cc_start: 0.8563 (p0) cc_final: 0.8309 (p0) REVERT: B 474 ASP cc_start: 0.7085 (m-30) cc_final: 0.6055 (t0) REVERT: B 509 MET cc_start: 0.8974 (mmm) cc_final: 0.8491 (mmm) REVERT: B 524 LYS cc_start: 0.7818 (tttt) cc_final: 0.7343 (mppt) REVERT: C 29 LYS cc_start: 0.8908 (mttp) cc_final: 0.8682 (mmtp) REVERT: C 156 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.7025 (mtp85) REVERT: C 180 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6827 (mm-30) REVERT: C 268 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7241 (tt0) REVERT: C 336 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: C 342 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: C 547 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6908 (tpt90) REVERT: D 52 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: D 62 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5889 (mt-10) REVERT: D 98 LYS cc_start: 0.7869 (tttt) cc_final: 0.7219 (mtpt) REVERT: D 162 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: D 216 ARG cc_start: 0.8534 (ptt-90) cc_final: 0.8210 (ptt180) REVERT: D 236 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8408 (mtt90) REVERT: D 248 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7574 (mm-30) REVERT: D 280 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7867 (ttp-110) REVERT: D 373 GLU cc_start: 0.7621 (pm20) cc_final: 0.7249 (pm20) REVERT: D 398 ILE cc_start: 0.8229 (mt) cc_final: 0.7872 (mm) REVERT: D 413 GLN cc_start: 0.8016 (mt0) cc_final: 0.7810 (mt0) REVERT: D 450 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6713 (mm-30) REVERT: D 453 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7866 (mtt180) REVERT: E 26 ASP cc_start: 0.7631 (m-30) cc_final: 0.7346 (m-30) REVERT: E 61 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6791 (pt0) REVERT: E 98 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7782 (mmtp) REVERT: E 200 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8180 (mt-10) REVERT: E 216 ARG cc_start: 0.8329 (ptt90) cc_final: 0.7897 (ptt-90) REVERT: E 274 ARG cc_start: 0.7991 (mtp180) cc_final: 0.6894 (mmp-170) REVERT: E 388 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8212 (t0) REVERT: E 394 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8111 (mttp) REVERT: F 25 LYS cc_start: 0.7096 (ptmm) cc_final: 0.6816 (mtpt) REVERT: F 53 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7495 (mm-30) REVERT: F 79 VAL cc_start: 0.8789 (p) cc_final: 0.8508 (m) REVERT: F 98 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8005 (mmtp) REVERT: F 125 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7383 (ttm170) REVERT: F 210 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7697 (ttt-90) REVERT: F 223 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8294 (mttp) REVERT: F 259 ASP cc_start: 0.7067 (t0) cc_final: 0.6854 (t70) REVERT: F 265 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7818 (tm-30) REVERT: F 334 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: F 362 MET cc_start: 0.8884 (ttt) cc_final: 0.8581 (ttt) REVERT: F 373 GLU cc_start: 0.7631 (mp0) cc_final: 0.7226 (pm20) REVERT: F 394 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7629 (mttt) REVERT: F 437 GLN cc_start: 0.8809 (tt0) cc_final: 0.8484 (tt0) REVERT: F 456 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7558 (mmmt) REVERT: F 465 GLN cc_start: 0.7656 (tt0) cc_final: 0.7441 (tt0) REVERT: G 38 GLU cc_start: 0.7864 (tt0) cc_final: 0.7578 (tp30) REVERT: G 47 MET cc_start: 0.7131 (tpp) cc_final: 0.6755 (mpp) REVERT: G 48 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6249 (mt-10) REVERT: G 139 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6001 (ttm170) REVERT: G 148 LYS cc_start: 0.7480 (mttt) cc_final: 0.7188 (mtpm) REVERT: G 156 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7772 (mttt) REVERT: G 159 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.7780 (mtm110) REVERT: G 166 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7210 (mt0) REVERT: G 198 LYS cc_start: 0.8250 (tttt) cc_final: 0.7500 (mptt) REVERT: H 36 LEU cc_start: 0.5456 (tt) cc_final: 0.4930 (pp) REVERT: H 90 MET cc_start: 0.6937 (tpp) cc_final: 0.6355 (tpp) REVERT: J 105 ARG cc_start: 0.4823 (mtt180) cc_final: 0.4427 (mmt-90) REVERT: J 109 LEU cc_start: 0.6257 (tp) cc_final: 0.5836 (mt) REVERT: J 115 LEU cc_start: 0.4378 (mm) cc_final: 0.4115 (mm) REVERT: J 121 LEU cc_start: 0.4570 (tp) cc_final: 0.4195 (mm) REVERT: J 126 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.4095 (mp0) REVERT: J 173 ARG cc_start: 0.6614 (ttt-90) cc_final: 0.6150 (ttm-80) REVERT: L 74 GLN cc_start: 0.6695 (tp40) cc_final: 0.6273 (tp40) REVERT: L 76 ARG cc_start: 0.6753 (mtp85) cc_final: 0.6445 (mtt180) REVERT: L 84 ARG cc_start: 0.6248 (ttm-80) cc_final: 0.5880 (ttm170) REVERT: L 85 ARG cc_start: 0.5885 (ttp-110) cc_final: 0.5645 (ttp-110) REVERT: L 153 ARG cc_start: 0.6087 (ttm170) cc_final: 0.5821 (ttp80) REVERT: L 160 LYS cc_start: 0.7331 (mttp) cc_final: 0.6504 (mmtp) REVERT: L 162 GLN cc_start: 0.7569 (pt0) cc_final: 0.6624 (pt0) REVERT: L 181 LYS cc_start: 0.6837 (mptm) cc_final: 0.6001 (mtpt) outliers start: 130 outliers final: 46 residues processed: 536 average time/residue: 0.9621 time to fit residues: 580.1013 Evaluate side-chains 490 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 418 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 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 21 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 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 E residue 61 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 98 LYS 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 125 ARG Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 334 GLU 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 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 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 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 106 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 311 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 304 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 344 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN B 397 GLN D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 170 GLN E 364 ASN E 413 GLN F 129 GLN G 180 GLN ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.102562 restraints weight = 32702.782| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.37 r_work: 0.2868 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 30023 Z= 0.330 Angle : 0.743 10.716 40670 Z= 0.386 Chirality : 0.053 0.208 4560 Planarity : 0.007 0.081 5330 Dihedral : 5.402 65.938 4185 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 4.96 % Allowed : 15.08 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.14), residues: 3764 helix: 1.16 (0.13), residues: 1575 sheet: -0.30 (0.21), residues: 586 loop : -0.04 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 196 TYR 0.022 0.003 TYR A 304 PHE 0.021 0.003 PHE E 414 TRP 0.018 0.003 TRP A 119 HIS 0.006 0.002 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00814 (30023) covalent geometry : angle 0.74267 (40670) hydrogen bonds : bond 0.06346 ( 1332) hydrogen bonds : angle 5.06385 ( 3807) *********************** 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 578 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 425 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: A 29 LYS cc_start: 0.8406 (mttt) cc_final: 0.8162 (mtpp) REVERT: A 53 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: A 109 HIS cc_start: 0.7906 (m-70) cc_final: 0.7567 (m170) REVERT: A 115 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8136 (tttp) REVERT: A 156 ARG cc_start: 0.6610 (ttp80) cc_final: 0.6240 (ttp80) REVERT: A 340 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7389 (mpt-90) REVERT: A 449 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 469 GLN cc_start: 0.7454 (mt0) cc_final: 0.6997 (mm110) REVERT: A 541 GLN cc_start: 0.6893 (mt0) cc_final: 0.6593 (mm-40) REVERT: B 19 MET cc_start: 0.8842 (mmm) cc_final: 0.8427 (mmm) REVERT: B 32 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: B 93 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7344 (mmm160) REVERT: B 122 MET cc_start: 0.8060 (mtm) cc_final: 0.7758 (mtt) REVERT: B 124 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6964 (mppt) REVERT: B 130 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7187 (ptm-80) REVERT: B 154 ARG cc_start: 0.7164 (mtp-110) cc_final: 0.6942 (ptp90) REVERT: B 158 LYS cc_start: 0.7519 (tttt) cc_final: 0.7302 (tttp) REVERT: B 276 LYS cc_start: 0.7539 (mmtt) cc_final: 0.7318 (mtmt) REVERT: B 391 MET cc_start: 0.7388 (mmp) cc_final: 0.7140 (mmt) REVERT: B 410 ASP cc_start: 0.8601 (p0) cc_final: 0.8301 (p0) REVERT: B 467 ILE cc_start: 0.7533 (mt) cc_final: 0.7220 (tp) REVERT: B 509 MET cc_start: 0.8970 (mmm) cc_final: 0.8496 (mmm) REVERT: B 524 LYS cc_start: 0.7813 (tttt) cc_final: 0.7300 (mppt) REVERT: C 3 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: C 29 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8678 (mmtm) REVERT: C 156 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.7139 (mmm-85) REVERT: C 180 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6790 (mm-30) REVERT: C 191 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8191 (mtm180) REVERT: C 336 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7967 (tp30) REVERT: C 342 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: C 480 GLU cc_start: 0.7544 (mp0) cc_final: 0.7010 (mp0) REVERT: C 547 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6852 (tpt90) REVERT: D 52 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: D 98 LYS cc_start: 0.7901 (tttt) cc_final: 0.7457 (mmmm) REVERT: D 106 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7868 (pt) REVERT: D 110 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7165 (ptmt) REVERT: D 128 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: D 162 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: D 280 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7292 (mtm-85) REVERT: D 334 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: D 398 ILE cc_start: 0.8196 (mt) cc_final: 0.7805 (mm) REVERT: D 413 GLN cc_start: 0.8031 (mt0) cc_final: 0.7788 (mt0) REVERT: D 420 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7419 (mmp-170) REVERT: D 450 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6769 (mm-30) REVERT: D 457 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.6073 (m-30) REVERT: E 26 ASP cc_start: 0.7780 (m-30) cc_final: 0.7457 (m-30) REVERT: E 36 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8050 (tttp) REVERT: E 61 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6900 (pt0) REVERT: E 98 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7759 (mmtp) REVERT: E 200 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8225 (mt-10) REVERT: E 216 ARG cc_start: 0.8387 (ptt90) cc_final: 0.7867 (ptt-90) REVERT: E 232 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8188 (pt) REVERT: E 274 ARG cc_start: 0.7938 (mtp180) cc_final: 0.6871 (mmp-170) REVERT: E 388 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8317 (t0) REVERT: E 452 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7662 (mmtp) REVERT: F 25 LYS cc_start: 0.7149 (ptmm) cc_final: 0.6807 (mtpt) REVERT: F 79 VAL cc_start: 0.8729 (p) cc_final: 0.8192 (t) REVERT: F 98 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7916 (mmtp) REVERT: F 125 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7420 (ttm170) REVERT: F 210 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7857 (ttt-90) REVERT: F 265 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7856 (tm-30) REVERT: F 334 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: F 373 GLU cc_start: 0.7659 (mp0) cc_final: 0.7281 (pm20) REVERT: F 394 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7666 (mttt) REVERT: F 437 GLN cc_start: 0.8855 (tt0) cc_final: 0.8639 (tt0) REVERT: F 465 GLN cc_start: 0.7579 (tt0) cc_final: 0.7040 (pt0) REVERT: G 38 GLU cc_start: 0.8029 (tt0) cc_final: 0.7666 (tp30) REVERT: G 47 MET cc_start: 0.7134 (tpp) cc_final: 0.6590 (tpp) REVERT: G 48 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6252 (mt-10) REVERT: G 139 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6028 (ttm170) REVERT: G 148 LYS cc_start: 0.7582 (mttt) cc_final: 0.7262 (mtpm) REVERT: G 156 LYS cc_start: 0.8433 (mtpp) cc_final: 0.7911 (mtmt) REVERT: G 159 ARG cc_start: 0.8436 (mtt-85) cc_final: 0.7829 (mtm110) REVERT: G 166 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: G 198 LYS cc_start: 0.8282 (tttt) cc_final: 0.7477 (mptt) REVERT: H 15 LEU cc_start: 0.5654 (tp) cc_final: 0.5421 (tp) REVERT: H 19 GLU cc_start: 0.4528 (tp30) cc_final: 0.4244 (tp30) REVERT: H 48 ASP cc_start: 0.5731 (OUTLIER) cc_final: 0.4773 (p0) REVERT: H 90 MET cc_start: 0.7014 (tpp) cc_final: 0.6648 (tpp) REVERT: J 105 ARG cc_start: 0.4728 (mtt180) cc_final: 0.4415 (mmt-90) REVERT: J 109 LEU cc_start: 0.6051 (tp) cc_final: 0.5720 (mt) REVERT: J 126 GLU cc_start: 0.4201 (OUTLIER) cc_final: 0.3846 (mp0) REVERT: J 160 LYS cc_start: 0.7564 (mtmm) cc_final: 0.7357 (mtmt) REVERT: L 61 GLU cc_start: 0.3664 (pt0) cc_final: 0.3432 (pt0) REVERT: L 74 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.5915 (mm-40) REVERT: L 76 ARG cc_start: 0.6890 (mtp85) cc_final: 0.6581 (mtt180) REVERT: L 84 ARG cc_start: 0.6291 (ttm-80) cc_final: 0.5928 (ttm170) REVERT: L 145 GLU cc_start: 0.5320 (mt-10) cc_final: 0.5093 (tt0) REVERT: L 160 LYS cc_start: 0.7506 (mttp) cc_final: 0.6614 (mmtm) REVERT: L 162 GLN cc_start: 0.7635 (pt0) cc_final: 0.6693 (pt0) outliers start: 153 outliers final: 55 residues processed: 522 average time/residue: 0.9621 time to fit residues: 565.6484 Evaluate side-chains 490 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 399 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 144 THR 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 449 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 557 GLU 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 226 ILE 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 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 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 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 110 LYS 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 280 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 334 GLU 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 98 LYS Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 334 GLU 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 48 ASP 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 74 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 334 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 E 363 ASN E 364 ASN E 413 GLN F 437 GLN J 162 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.103850 restraints weight = 32694.654| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.47 r_work: 0.2895 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3308 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= 0.158 Angle : 0.561 10.194 40670 Z= 0.291 Chirality : 0.045 0.200 4560 Planarity : 0.005 0.049 5330 Dihedral : 4.885 64.075 4185 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.17 % Rotamer: Outliers : 4.09 % Allowed : 16.54 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.14), residues: 3764 helix: 1.53 (0.13), residues: 1581 sheet: -0.32 (0.21), residues: 574 loop : 0.05 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 156 TYR 0.017 0.002 TYR H 89 PHE 0.018 0.002 PHE E 130 TRP 0.012 0.001 TRP A 119 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00378 (30023) covalent geometry : angle 0.56089 (40670) hydrogen bonds : bond 0.04793 ( 1332) hydrogen bonds : angle 4.70628 ( 3807) *********************** 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 544 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 418 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7739 (mmm) REVERT: A 29 LYS cc_start: 0.8427 (mttt) cc_final: 0.8161 (mtpp) REVERT: A 53 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: A 109 HIS cc_start: 0.7848 (m-70) cc_final: 0.7492 (m170) REVERT: A 115 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8164 (tttp) REVERT: A 154 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6963 (mtp85) REVERT: A 156 ARG cc_start: 0.6578 (ttp80) cc_final: 0.6216 (ttp80) REVERT: A 340 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7322 (mpt-90) REVERT: A 449 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 469 GLN cc_start: 0.7444 (mt0) cc_final: 0.6968 (mm110) REVERT: A 498 ASN cc_start: 0.8827 (t0) cc_final: 0.8606 (t0) REVERT: A 541 GLN cc_start: 0.6890 (mt0) cc_final: 0.6630 (mm-40) REVERT: B 32 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: B 93 ARG cc_start: 0.7578 (mtp180) cc_final: 0.7290 (mmm160) REVERT: B 122 MET cc_start: 0.8146 (mtm) cc_final: 0.7893 (mtt) REVERT: B 124 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6952 (mppt) REVERT: B 130 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7114 (ptm-80) REVERT: B 154 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6839 (ptp90) REVERT: B 156 ARG cc_start: 0.7128 (mtp85) cc_final: 0.6331 (tpp80) REVERT: B 158 LYS cc_start: 0.7477 (tttt) cc_final: 0.7021 (tttt) REVERT: B 276 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7321 (mtmt) REVERT: B 391 MET cc_start: 0.7522 (mmp) cc_final: 0.7179 (mmt) REVERT: B 410 ASP cc_start: 0.8570 (p0) cc_final: 0.8231 (p0) REVERT: B 467 ILE cc_start: 0.7398 (mt) cc_final: 0.7078 (tp) REVERT: B 524 LYS cc_start: 0.7771 (tttt) cc_final: 0.7210 (mppt) REVERT: C 3 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: C 29 LYS cc_start: 0.8956 (mttp) cc_final: 0.8732 (mmtp) REVERT: C 129 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7457 (m) REVERT: C 156 ARG cc_start: 0.7389 (ttm-80) cc_final: 0.7135 (mmm-85) REVERT: C 180 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6851 (mm-30) REVERT: C 336 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: C 342 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: C 410 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8255 (t0) REVERT: C 467 ILE cc_start: 0.7149 (mt) cc_final: 0.6929 (mm) REVERT: C 547 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6834 (tpt90) REVERT: D 98 LYS cc_start: 0.7867 (tttt) cc_final: 0.7388 (mmmm) REVERT: D 128 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: D 162 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: D 248 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7497 (mm-30) REVERT: D 280 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7859 (ttp-110) REVERT: D 398 ILE cc_start: 0.8284 (mt) cc_final: 0.7986 (mm) REVERT: D 413 GLN cc_start: 0.7984 (mt0) cc_final: 0.7732 (mt0) REVERT: D 420 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7405 (mmt-90) REVERT: D 450 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6741 (mm-30) REVERT: D 457 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6107 (m-30) REVERT: E 26 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: E 61 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6879 (pt0) REVERT: E 200 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8147 (mt-10) REVERT: E 207 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: E 216 ARG cc_start: 0.8385 (ptt90) cc_final: 0.7921 (ptt-90) REVERT: E 274 ARG cc_start: 0.7884 (mtp180) cc_final: 0.6835 (mmp-170) REVERT: E 388 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8232 (t0) REVERT: E 394 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8033 (mttp) REVERT: F 25 LYS cc_start: 0.7094 (ptmm) cc_final: 0.6803 (mtpt) REVERT: F 53 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7544 (mm-30) REVERT: F 79 VAL cc_start: 0.8693 (p) cc_final: 0.8317 (m) REVERT: F 98 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7829 (mmtp) REVERT: F 125 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7351 (ttm170) REVERT: F 210 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7812 (ttt-90) REVERT: F 265 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7797 (tm-30) REVERT: F 373 GLU cc_start: 0.7621 (mp0) cc_final: 0.7249 (pm20) REVERT: F 394 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7616 (mttt) REVERT: G 38 GLU cc_start: 0.7997 (tt0) cc_final: 0.7642 (tp30) REVERT: G 47 MET cc_start: 0.7084 (tpp) cc_final: 0.6670 (tpp) REVERT: G 48 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6192 (mt-10) REVERT: G 139 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.5963 (ttm170) REVERT: G 148 LYS cc_start: 0.7550 (mttt) cc_final: 0.7235 (mtpm) REVERT: G 156 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7831 (mttt) REVERT: G 159 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.7793 (mtm110) REVERT: G 166 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: G 198 LYS cc_start: 0.8266 (tttt) cc_final: 0.7436 (mptt) REVERT: H 15 LEU cc_start: 0.5558 (tp) cc_final: 0.5300 (tp) REVERT: H 19 GLU cc_start: 0.4477 (tp30) cc_final: 0.4197 (tp30) REVERT: H 90 MET cc_start: 0.7039 (tpp) cc_final: 0.6644 (tpp) REVERT: J 105 ARG cc_start: 0.4744 (mtt180) cc_final: 0.4406 (mmt-90) REVERT: J 109 LEU cc_start: 0.6026 (tp) cc_final: 0.5725 (mt) REVERT: J 121 LEU cc_start: 0.4564 (tp) cc_final: 0.4053 (mm) REVERT: L 74 GLN cc_start: 0.6591 (tp40) cc_final: 0.5900 (mm-40) REVERT: L 76 ARG cc_start: 0.6895 (mtp85) cc_final: 0.6593 (mtt180) REVERT: L 84 ARG cc_start: 0.6249 (ttm-80) cc_final: 0.5664 (ttt180) REVERT: L 145 GLU cc_start: 0.5316 (mt-10) cc_final: 0.4978 (tt0) REVERT: L 160 LYS cc_start: 0.7471 (mttp) cc_final: 0.6594 (mmtm) REVERT: L 162 GLN cc_start: 0.7694 (pt0) cc_final: 0.6701 (pt0) outliers start: 126 outliers final: 48 residues processed: 496 average time/residue: 0.8833 time to fit residues: 494.9057 Evaluate side-chains 473 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 396 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 133 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 154 ARG 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 449 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 154 ARG Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 267 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 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 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 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 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 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 26 ASP Chi-restraints excluded: chain E residue 61 GLU 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 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 37 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 111 VAL 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 128 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 166 GLN F 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.142341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.105608 restraints weight = 32643.037| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.50 r_work: 0.2892 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3400 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= 0.125 Angle : 0.518 10.449 40670 Z= 0.267 Chirality : 0.043 0.186 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.587 64.911 4185 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 3.37 % Allowed : 17.55 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.14), residues: 3764 helix: 1.80 (0.13), residues: 1568 sheet: -0.29 (0.21), residues: 586 loop : 0.22 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 481 TYR 0.016 0.001 TYR H 89 PHE 0.019 0.001 PHE A 574 TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00292 (30023) covalent geometry : angle 0.51799 (40670) hydrogen bonds : bond 0.04238 ( 1332) hydrogen bonds : angle 4.52264 ( 3807) *********************** 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 521 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 417 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7679 (mmm) REVERT: A 29 LYS cc_start: 0.8401 (mttt) cc_final: 0.8145 (mtpp) REVERT: A 53 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: A 109 HIS cc_start: 0.7793 (m-70) cc_final: 0.7449 (m170) REVERT: A 156 ARG cc_start: 0.6616 (ttp80) cc_final: 0.6249 (ttp80) REVERT: A 340 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7331 (mpt-90) REVERT: A 445 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: A 449 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 469 GLN cc_start: 0.7415 (mt0) cc_final: 0.6938 (mm110) REVERT: B 19 MET cc_start: 0.8831 (mmm) cc_final: 0.8162 (mmm) REVERT: B 32 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: B 93 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7292 (mmm160) REVERT: B 96 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 122 MET cc_start: 0.8088 (mtm) cc_final: 0.7853 (mtt) REVERT: B 124 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6983 (mppt) REVERT: B 130 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7098 (ptm-80) REVERT: B 154 ARG cc_start: 0.7137 (mtp-110) cc_final: 0.6871 (ptp90) REVERT: B 158 LYS cc_start: 0.7495 (tttt) cc_final: 0.7275 (tttp) REVERT: B 276 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7055 (ptmt) REVERT: B 391 MET cc_start: 0.7550 (mmp) cc_final: 0.7313 (mmt) REVERT: B 410 ASP cc_start: 0.8539 (p0) cc_final: 0.8237 (p0) REVERT: B 467 ILE cc_start: 0.7355 (mt) cc_final: 0.7068 (tp) REVERT: B 509 MET cc_start: 0.8992 (mmm) cc_final: 0.8634 (mmm) REVERT: B 524 LYS cc_start: 0.7768 (tttt) cc_final: 0.7259 (mppt) REVERT: C 29 LYS cc_start: 0.8886 (mttp) cc_final: 0.8664 (mmtp) REVERT: C 129 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7399 (m) REVERT: C 156 ARG cc_start: 0.7357 (ttm-80) cc_final: 0.7100 (mmm-85) REVERT: C 180 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6838 (mm-30) REVERT: C 191 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8158 (mtm180) REVERT: C 336 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: C 342 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: C 348 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: C 410 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 467 ILE cc_start: 0.7183 (mt) cc_final: 0.6970 (mm) REVERT: C 547 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6814 (tpt90) REVERT: D 98 LYS cc_start: 0.7906 (tttt) cc_final: 0.7411 (mmmt) REVERT: D 128 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7366 (pp20) REVERT: D 162 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: D 236 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8378 (mtt90) REVERT: D 248 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7506 (mm-30) REVERT: D 280 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7884 (ttp-110) REVERT: D 398 ILE cc_start: 0.8297 (mt) cc_final: 0.8041 (mm) REVERT: D 413 GLN cc_start: 0.8054 (mt0) cc_final: 0.7793 (mt0) REVERT: D 420 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7476 (mmt-90) REVERT: D 450 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6728 (mm-30) REVERT: D 457 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6101 (m-30) REVERT: E 26 ASP cc_start: 0.7722 (m-30) cc_final: 0.7427 (m-30) REVERT: E 61 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6918 (pt0) REVERT: E 200 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8172 (mt-10) REVERT: E 207 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: E 216 ARG cc_start: 0.8357 (ptt90) cc_final: 0.7927 (ptt-90) REVERT: E 274 ARG cc_start: 0.7947 (mtp180) cc_final: 0.6859 (mmp-170) REVERT: E 376 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7236 (tmtm) REVERT: E 388 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8199 (t0) REVERT: E 394 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8080 (mttp) REVERT: F 25 LYS cc_start: 0.7071 (ptmm) cc_final: 0.6815 (mtpt) REVERT: F 53 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7561 (mm-30) REVERT: F 79 VAL cc_start: 0.8665 (p) cc_final: 0.8308 (m) REVERT: F 98 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7765 (mmtp) REVERT: F 125 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7317 (ttm170) REVERT: F 210 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7805 (ttt-90) REVERT: F 265 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7772 (tm-30) REVERT: F 373 GLU cc_start: 0.7633 (mp0) cc_final: 0.7265 (pm20) REVERT: F 380 ASP cc_start: 0.8432 (m-30) cc_final: 0.7806 (m-30) REVERT: F 394 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7666 (mttt) REVERT: G 38 GLU cc_start: 0.8003 (tt0) cc_final: 0.7670 (tp30) REVERT: G 47 MET cc_start: 0.7014 (tpp) cc_final: 0.6624 (tpp) REVERT: G 48 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6252 (mt-10) REVERT: G 139 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.5898 (ttm170) REVERT: G 148 LYS cc_start: 0.7592 (mttt) cc_final: 0.7277 (mtpm) REVERT: G 156 LYS cc_start: 0.8346 (mtpp) cc_final: 0.7812 (mttt) REVERT: G 159 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.7790 (mtm110) REVERT: G 166 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7063 (mt0) REVERT: G 198 LYS cc_start: 0.8296 (tttt) cc_final: 0.7492 (mptt) REVERT: H 19 GLU cc_start: 0.4440 (tp30) cc_final: 0.4160 (tp30) REVERT: H 44 LEU cc_start: 0.6723 (tp) cc_final: 0.6425 (tp) REVERT: H 48 ASP cc_start: 0.5754 (OUTLIER) cc_final: 0.4705 (p0) REVERT: H 90 MET cc_start: 0.7003 (tpp) cc_final: 0.6551 (tpp) REVERT: J 105 ARG cc_start: 0.4768 (mtt180) cc_final: 0.4415 (mmt-90) REVERT: J 109 LEU cc_start: 0.5925 (tp) cc_final: 0.5638 (mt) REVERT: J 121 LEU cc_start: 0.4610 (tp) cc_final: 0.4161 (mm) REVERT: L 74 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5831 (mm110) REVERT: L 76 ARG cc_start: 0.6920 (mtp85) cc_final: 0.6624 (mtt180) REVERT: L 81 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6040 (tp30) REVERT: L 84 ARG cc_start: 0.6230 (ttm-80) cc_final: 0.5826 (ttm170) REVERT: L 145 GLU cc_start: 0.5412 (mt-10) cc_final: 0.5061 (tt0) REVERT: L 160 LYS cc_start: 0.7494 (mttp) cc_final: 0.6493 (mmtp) REVERT: L 162 GLN cc_start: 0.7704 (pt0) cc_final: 0.6692 (pt0) outliers start: 104 outliers final: 45 residues processed: 482 average time/residue: 0.9363 time to fit residues: 507.6320 Evaluate side-chains 474 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 398 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 536 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 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 532 ARG 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 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 402 ILE Chi-restraints excluded: chain C residue 410 ASP 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 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 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 42 VAL Chi-restraints excluded: chain E residue 61 GLU 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 F residue 23 ASN Chi-restraints excluded: chain F residue 106 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 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 J residue 168 LEU 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 228 optimal weight: 6.9990 chunk 319 optimal weight: 0.0170 chunk 254 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 345 optimal weight: 0.0670 chunk 349 optimal weight: 4.9990 chunk 315 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 336 optimal weight: 6.9990 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN E 129 GLN E 413 GLN F 166 GLN H 84 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.141241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.105000 restraints weight = 32732.674| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.49 r_work: 0.2892 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3454 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= 0.152 Angle : 0.545 10.251 40670 Z= 0.281 Chirality : 0.044 0.186 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.668 65.718 4185 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.14 % Rotamer: Outliers : 3.76 % Allowed : 17.48 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.14), residues: 3764 helix: 1.79 (0.13), residues: 1576 sheet: -0.25 (0.21), residues: 592 loop : 0.23 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 481 TYR 0.015 0.001 TYR H 89 PHE 0.017 0.002 PHE C 559 TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00364 (30023) covalent geometry : angle 0.54545 (40670) hydrogen bonds : bond 0.04511 ( 1332) hydrogen bonds : angle 4.56118 ( 3807) *********************** 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 519 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 403 time to evaluate : 1.238 Fit side-chains REVERT: A 19 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7684 (mmm) REVERT: A 29 LYS cc_start: 0.8401 (mttt) cc_final: 0.8137 (mtpp) REVERT: A 53 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7404 (mt-10) REVERT: A 109 HIS cc_start: 0.7824 (m-70) cc_final: 0.7496 (m170) REVERT: A 156 ARG cc_start: 0.6603 (ttp80) cc_final: 0.6253 (ttp80) REVERT: A 340 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7273 (mpt-90) REVERT: A 445 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: A 449 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: B 19 MET cc_start: 0.8822 (mmm) cc_final: 0.8145 (mmm) REVERT: B 32 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: B 93 ARG cc_start: 0.7544 (mtp180) cc_final: 0.7227 (mmm160) REVERT: B 96 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6675 (mt-10) REVERT: B 122 MET cc_start: 0.8092 (mtm) cc_final: 0.7862 (mtt) REVERT: B 124 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7007 (mppt) REVERT: B 130 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7070 (ptm-80) REVERT: B 154 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6879 (ptp90) REVERT: B 276 LYS cc_start: 0.7550 (mmtt) cc_final: 0.7019 (ptmt) REVERT: B 391 MET cc_start: 0.7524 (mmp) cc_final: 0.7275 (mmt) REVERT: B 410 ASP cc_start: 0.8529 (p0) cc_final: 0.8207 (p0) REVERT: B 467 ILE cc_start: 0.7353 (mt) cc_final: 0.7064 (tp) REVERT: B 524 LYS cc_start: 0.7731 (tttt) cc_final: 0.7240 (mppt) REVERT: C 29 LYS cc_start: 0.8873 (mttp) cc_final: 0.8638 (mmtp) REVERT: C 43 ASP cc_start: 0.8557 (t0) cc_final: 0.8342 (t0) REVERT: C 156 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.7129 (mmm-85) REVERT: C 180 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6786 (mm-30) REVERT: C 191 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8161 (mtm180) REVERT: C 336 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: C 342 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: C 344 MET cc_start: 0.8958 (mmp) cc_final: 0.8706 (mmm) REVERT: C 348 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: C 467 ILE cc_start: 0.7212 (mt) cc_final: 0.6982 (mm) REVERT: C 547 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6795 (tpt90) REVERT: D 62 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5920 (mt-10) REVERT: D 98 LYS cc_start: 0.7877 (tttt) cc_final: 0.7283 (mmtt) REVERT: D 106 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7886 (pt) REVERT: D 128 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: D 162 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: D 236 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8380 (mtt90) REVERT: D 248 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7504 (mm-30) REVERT: D 280 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7861 (ttp-110) REVERT: D 398 ILE cc_start: 0.8304 (mt) cc_final: 0.8047 (mm) REVERT: D 413 GLN cc_start: 0.8033 (mt0) cc_final: 0.7780 (mt0) REVERT: D 420 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7417 (mmt-90) REVERT: D 457 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6082 (m-30) REVERT: E 26 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: E 61 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6916 (pt0) REVERT: E 103 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7724 (mp) REVERT: E 200 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8126 (mt-10) REVERT: E 211 THR cc_start: 0.8426 (p) cc_final: 0.8202 (m) REVERT: E 216 ARG cc_start: 0.8364 (ptt90) cc_final: 0.7923 (ptt-90) REVERT: E 274 ARG cc_start: 0.7908 (mtp180) cc_final: 0.6872 (mmp-170) REVERT: E 376 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7219 (tmtm) REVERT: E 388 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8193 (t0) REVERT: E 394 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8077 (mttp) REVERT: F 25 LYS cc_start: 0.7034 (ptmm) cc_final: 0.6785 (mtpt) REVERT: F 53 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7583 (mm-30) REVERT: F 79 VAL cc_start: 0.8728 (p) cc_final: 0.8188 (t) REVERT: F 98 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7774 (mmtp) REVERT: F 125 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7312 (ttm170) REVERT: F 210 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7804 (ttt-90) REVERT: F 265 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7861 (tm-30) REVERT: F 373 GLU cc_start: 0.7584 (mp0) cc_final: 0.7226 (pm20) REVERT: F 380 ASP cc_start: 0.8405 (m-30) cc_final: 0.7753 (m-30) REVERT: F 394 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7635 (mttt) REVERT: F 421 PHE cc_start: 0.8844 (m-80) cc_final: 0.8608 (m-80) REVERT: G 38 GLU cc_start: 0.7967 (tt0) cc_final: 0.7629 (tp30) REVERT: G 47 MET cc_start: 0.7094 (tpp) cc_final: 0.6761 (tpp) REVERT: G 48 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6235 (mt-10) REVERT: G 139 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5880 (ttm170) REVERT: G 148 LYS cc_start: 0.7583 (mttt) cc_final: 0.7295 (mtpm) REVERT: G 156 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7801 (mttt) REVERT: G 159 ARG cc_start: 0.8374 (mtt-85) cc_final: 0.7798 (mtm110) REVERT: G 166 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: G 198 LYS cc_start: 0.8236 (tttt) cc_final: 0.7336 (mptp) REVERT: H 15 LEU cc_start: 0.5505 (tp) cc_final: 0.5192 (tp) REVERT: H 19 GLU cc_start: 0.4520 (tp30) cc_final: 0.4215 (tp30) REVERT: H 48 ASP cc_start: 0.5720 (OUTLIER) cc_final: 0.4669 (p0) REVERT: H 90 MET cc_start: 0.7085 (tpp) cc_final: 0.6673 (tpt) REVERT: J 88 ARG cc_start: 0.5287 (ptm-80) cc_final: 0.5054 (ptm-80) REVERT: J 105 ARG cc_start: 0.4758 (mtt180) cc_final: 0.4407 (mmt-90) REVERT: J 109 LEU cc_start: 0.5908 (tp) cc_final: 0.5610 (mt) REVERT: L 74 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.5882 (mm-40) REVERT: L 76 ARG cc_start: 0.6876 (mtp85) cc_final: 0.6579 (mtt180) REVERT: L 84 ARG cc_start: 0.6222 (ttm-80) cc_final: 0.5796 (ttm170) REVERT: L 145 GLU cc_start: 0.5262 (mt-10) cc_final: 0.4883 (tt0) REVERT: L 160 LYS cc_start: 0.7514 (mttp) cc_final: 0.6659 (mmtm) REVERT: L 162 GLN cc_start: 0.7661 (pt0) cc_final: 0.6650 (pt0) outliers start: 116 outliers final: 56 residues processed: 472 average time/residue: 0.8783 time to fit residues: 467.2375 Evaluate side-chains 487 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 398 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 536 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 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 154 ARG 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 532 ARG 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 412 SER 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 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 259 ASP 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 103 LEU Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 137 THR 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 32 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 320 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN H 84 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.141509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.105233 restraints weight = 32833.400| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.47 r_work: 0.2890 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 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 : 0.004 0.041 30023 Z= 0.155 Angle : 0.549 10.244 40670 Z= 0.283 Chirality : 0.044 0.190 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.669 65.408 4185 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.14 % Rotamer: Outliers : 3.80 % Allowed : 17.68 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.14), residues: 3764 helix: 1.80 (0.13), residues: 1570 sheet: -0.30 (0.21), residues: 586 loop : 0.21 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 88 TYR 0.015 0.002 TYR H 89 PHE 0.017 0.002 PHE C 559 TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00372 (30023) covalent geometry : angle 0.54897 (40670) hydrogen bonds : bond 0.04507 ( 1332) hydrogen bonds : angle 4.56038 ( 3807) *********************** 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 521 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 404 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: A 29 LYS cc_start: 0.8393 (mttt) cc_final: 0.8139 (mtpp) REVERT: A 53 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: A 109 HIS cc_start: 0.7827 (m-70) cc_final: 0.7512 (m170) REVERT: A 156 ARG cc_start: 0.6608 (ttp80) cc_final: 0.6254 (ttp80) REVERT: A 340 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7324 (mpt-90) REVERT: A 445 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: A 449 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: B 17 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8190 (ttpt) REVERT: B 19 MET cc_start: 0.8817 (mmm) cc_final: 0.8136 (mmm) REVERT: B 32 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7126 (mm-30) REVERT: B 93 ARG cc_start: 0.7535 (mtp180) cc_final: 0.7226 (mmm160) REVERT: B 96 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6685 (mt-10) REVERT: B 122 MET cc_start: 0.8072 (mtm) cc_final: 0.7848 (mtt) REVERT: B 124 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7013 (mppt) REVERT: B 130 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7088 (ptm-80) REVERT: B 154 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6869 (ptp90) REVERT: B 276 LYS cc_start: 0.7494 (mmtt) cc_final: 0.6981 (ptmt) REVERT: B 391 MET cc_start: 0.7537 (mmp) cc_final: 0.7278 (mmt) REVERT: B 410 ASP cc_start: 0.8564 (p0) cc_final: 0.8243 (p0) REVERT: B 467 ILE cc_start: 0.7390 (mt) cc_final: 0.7099 (tp) REVERT: B 524 LYS cc_start: 0.7781 (tttt) cc_final: 0.7228 (mppt) REVERT: C 29 LYS cc_start: 0.8871 (mttp) cc_final: 0.8628 (mmtp) REVERT: C 43 ASP cc_start: 0.8538 (t0) cc_final: 0.8318 (t0) REVERT: C 156 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.7130 (mmm-85) REVERT: C 180 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6747 (mm-30) REVERT: C 191 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8159 (mtm180) REVERT: C 336 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: C 342 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: C 348 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: C 467 ILE cc_start: 0.7195 (mt) cc_final: 0.6978 (mm) REVERT: C 547 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6790 (tpt90) REVERT: D 52 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: D 62 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5907 (mt-10) REVERT: D 98 LYS cc_start: 0.7873 (tttt) cc_final: 0.7279 (mmtt) REVERT: D 106 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7886 (pt) REVERT: D 128 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7332 (pp20) REVERT: D 162 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: D 236 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8401 (mtt90) REVERT: D 248 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7502 (mm-30) REVERT: D 280 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7856 (ttp-110) REVERT: D 398 ILE cc_start: 0.8307 (mt) cc_final: 0.8044 (mm) REVERT: D 413 GLN cc_start: 0.8055 (mt0) cc_final: 0.7846 (mt0) REVERT: D 420 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7411 (mmt-90) REVERT: D 457 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6075 (m-30) REVERT: E 26 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: E 61 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6924 (pt0) REVERT: E 98 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7727 (mmtp) REVERT: E 103 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7732 (mp) REVERT: E 194 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7937 (mpp) REVERT: E 200 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8123 (mt-10) REVERT: E 207 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: E 211 THR cc_start: 0.8429 (p) cc_final: 0.8207 (m) REVERT: E 216 ARG cc_start: 0.8372 (ptt90) cc_final: 0.7938 (ptt-90) REVERT: E 274 ARG cc_start: 0.7899 (mtp180) cc_final: 0.6865 (mmp-170) REVERT: E 376 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7232 (tmtm) REVERT: E 388 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8193 (t0) REVERT: E 452 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7620 (mmtp) REVERT: F 25 LYS cc_start: 0.7081 (ptmm) cc_final: 0.6809 (mtpt) REVERT: F 53 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7576 (mm-30) REVERT: F 79 VAL cc_start: 0.8734 (p) cc_final: 0.8204 (t) REVERT: F 98 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7773 (mmtp) REVERT: F 125 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7327 (ttm170) REVERT: F 210 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7807 (ttt-90) REVERT: F 265 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7780 (tm-30) REVERT: F 373 GLU cc_start: 0.7576 (mp0) cc_final: 0.7216 (pm20) REVERT: F 380 ASP cc_start: 0.8413 (m-30) cc_final: 0.7755 (m-30) REVERT: F 394 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7632 (mttt) REVERT: G 38 GLU cc_start: 0.7968 (tt0) cc_final: 0.7631 (tp30) REVERT: G 47 MET cc_start: 0.7073 (tpp) cc_final: 0.6745 (tpp) REVERT: G 48 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6191 (mt-10) REVERT: G 139 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5872 (ttm170) REVERT: G 148 LYS cc_start: 0.7575 (mttt) cc_final: 0.7290 (mtpm) REVERT: G 156 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7809 (mttt) REVERT: G 159 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.7819 (mtm110) REVERT: G 166 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7174 (mt0) REVERT: G 198 LYS cc_start: 0.8269 (tttt) cc_final: 0.7392 (mptp) REVERT: H 19 GLU cc_start: 0.4577 (tp30) cc_final: 0.4261 (tp30) REVERT: H 48 ASP cc_start: 0.5705 (OUTLIER) cc_final: 0.4658 (p0) REVERT: H 90 MET cc_start: 0.7100 (tpp) cc_final: 0.6704 (tpt) REVERT: I 107 LEU cc_start: 0.5157 (OUTLIER) cc_final: 0.4944 (tt) REVERT: J 88 ARG cc_start: 0.5268 (ptm-80) cc_final: 0.5044 (ptm-80) REVERT: J 105 ARG cc_start: 0.4724 (mtt180) cc_final: 0.4391 (mmt-90) REVERT: J 109 LEU cc_start: 0.5896 (tp) cc_final: 0.5599 (mt) REVERT: J 121 LEU cc_start: 0.4766 (mt) cc_final: 0.4255 (mm) REVERT: L 74 GLN cc_start: 0.6562 (OUTLIER) cc_final: 0.5880 (mm-40) REVERT: L 76 ARG cc_start: 0.6856 (mtp85) cc_final: 0.6565 (mtt180) REVERT: L 81 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6026 (tp30) REVERT: L 84 ARG cc_start: 0.6226 (ttm-80) cc_final: 0.5829 (ttm170) REVERT: L 145 GLU cc_start: 0.5175 (mt-10) cc_final: 0.4779 (tt0) REVERT: L 160 LYS cc_start: 0.7518 (mttp) cc_final: 0.6640 (mmtm) REVERT: L 162 GLN cc_start: 0.7659 (pt0) cc_final: 0.6641 (pt0) outliers start: 117 outliers final: 62 residues processed: 477 average time/residue: 0.8642 time to fit residues: 464.8014 Evaluate side-chains 500 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 398 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 527 GLU Chi-restraints excluded: chain A residue 536 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 17 LYS 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 97 LYS 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 154 ARG 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 532 ARG 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 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 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 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 98 LYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 194 MET 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 86 LYS Chi-restraints excluded: chain F residue 106 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 37 VAL 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 139 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 275 optimal weight: 0.5980 chunk 237 optimal weight: 0.0070 chunk 201 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- 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 ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN H 84 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.141727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.105621 restraints weight = 32807.461| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.49 r_work: 0.2893 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30023 Z= 0.146 Angle : 0.541 10.509 40670 Z= 0.278 Chirality : 0.044 0.189 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.628 65.363 4185 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 3.80 % Allowed : 17.84 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.14), residues: 3764 helix: 1.82 (0.13), residues: 1568 sheet: -0.25 (0.21), residues: 592 loop : 0.25 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 88 TYR 0.014 0.001 TYR H 89 PHE 0.017 0.002 PHE C 559 TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00348 (30023) covalent geometry : angle 0.54100 (40670) hydrogen bonds : bond 0.04405 ( 1332) hydrogen bonds : angle 4.53464 ( 3807) *********************** 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 522 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 405 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7673 (mmm) REVERT: A 29 LYS cc_start: 0.8390 (mttt) cc_final: 0.8137 (mtpp) REVERT: A 53 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: A 109 HIS cc_start: 0.7838 (m-70) cc_final: 0.7507 (m170) REVERT: A 156 ARG cc_start: 0.6603 (ttp80) cc_final: 0.6249 (ttp80) REVERT: A 340 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7348 (mpt-90) REVERT: A 445 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: A 449 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: B 17 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8289 (ttpt) REVERT: B 19 MET cc_start: 0.8815 (mmm) cc_final: 0.8330 (mmm) REVERT: B 32 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: B 93 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7230 (mmm160) REVERT: B 96 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6666 (mt-10) REVERT: B 122 MET cc_start: 0.8067 (mtm) cc_final: 0.7848 (mtt) REVERT: B 124 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6964 (mppt) REVERT: B 130 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7067 (ptm-80) REVERT: B 154 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6857 (ptp90) REVERT: B 276 LYS cc_start: 0.7475 (mmtt) cc_final: 0.6913 (ptmt) REVERT: B 391 MET cc_start: 0.7545 (mmp) cc_final: 0.7284 (mmt) REVERT: B 410 ASP cc_start: 0.8544 (p0) cc_final: 0.8238 (p0) REVERT: B 467 ILE cc_start: 0.7386 (mt) cc_final: 0.7098 (tp) REVERT: B 509 MET cc_start: 0.8898 (mmm) cc_final: 0.8545 (mmm) REVERT: B 524 LYS cc_start: 0.7727 (tttt) cc_final: 0.7230 (mppt) REVERT: C 29 LYS cc_start: 0.8871 (mttp) cc_final: 0.8624 (mmtp) REVERT: C 43 ASP cc_start: 0.8538 (t0) cc_final: 0.8322 (t0) REVERT: C 156 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.7124 (mmm-85) REVERT: C 180 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6715 (mm-30) REVERT: C 191 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8152 (mtm180) REVERT: C 336 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: C 342 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: C 348 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: C 467 ILE cc_start: 0.7195 (mt) cc_final: 0.6981 (mm) REVERT: C 547 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6796 (tpt90) REVERT: D 52 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: D 62 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5908 (mt-10) REVERT: D 98 LYS cc_start: 0.7864 (tttt) cc_final: 0.7135 (mtpt) REVERT: D 106 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7901 (pt) REVERT: D 162 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: D 236 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8395 (mtt90) REVERT: D 248 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7498 (mm-30) REVERT: D 280 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7848 (ttp-110) REVERT: D 398 ILE cc_start: 0.8308 (mt) cc_final: 0.8060 (mm) REVERT: D 413 GLN cc_start: 0.8041 (mt0) cc_final: 0.7828 (mt0) REVERT: D 420 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7405 (mmt-90) REVERT: D 457 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6064 (m-30) REVERT: E 26 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: E 61 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: E 98 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7727 (mmtp) REVERT: E 103 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7751 (mp) REVERT: E 194 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7915 (mpp) REVERT: E 200 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8130 (mt-10) REVERT: E 207 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: E 211 THR cc_start: 0.8413 (p) cc_final: 0.8195 (m) REVERT: E 216 ARG cc_start: 0.8375 (ptt90) cc_final: 0.7941 (ptt-90) REVERT: E 274 ARG cc_start: 0.7884 (mtp180) cc_final: 0.6861 (mmp-170) REVERT: E 376 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7254 (tmtm) REVERT: E 388 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8197 (t0) REVERT: E 452 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7620 (mmtp) REVERT: F 25 LYS cc_start: 0.7039 (ptmm) cc_final: 0.6782 (mtpt) REVERT: F 53 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7568 (mm-30) REVERT: F 79 VAL cc_start: 0.8731 (p) cc_final: 0.8211 (t) REVERT: F 98 LYS cc_start: 0.8313 (mmtt) cc_final: 0.7833 (mmtp) REVERT: F 125 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7327 (ttm170) REVERT: F 210 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7805 (ttt-90) REVERT: F 265 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7829 (tm-30) REVERT: F 373 GLU cc_start: 0.7561 (mp0) cc_final: 0.7206 (pm20) REVERT: F 380 ASP cc_start: 0.8431 (m-30) cc_final: 0.7770 (m-30) REVERT: F 394 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7600 (mttt) REVERT: G 38 GLU cc_start: 0.7964 (tt0) cc_final: 0.7632 (tp30) REVERT: G 47 MET cc_start: 0.7090 (tpp) cc_final: 0.6796 (tpp) REVERT: G 48 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6236 (mt-10) REVERT: G 139 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.5869 (ttm170) REVERT: G 148 LYS cc_start: 0.7578 (mttt) cc_final: 0.7308 (mtpm) REVERT: G 156 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7821 (mttt) REVERT: G 159 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.7814 (mtm110) REVERT: G 166 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: G 198 LYS cc_start: 0.8275 (tttt) cc_final: 0.7399 (mptp) REVERT: H 15 LEU cc_start: 0.5539 (tp) cc_final: 0.5218 (tp) REVERT: H 19 GLU cc_start: 0.4530 (tp30) cc_final: 0.4214 (tp30) REVERT: H 44 LEU cc_start: 0.6697 (tp) cc_final: 0.6436 (tp) REVERT: H 48 ASP cc_start: 0.5665 (OUTLIER) cc_final: 0.4641 (p0) REVERT: H 63 MET cc_start: 0.4684 (mmp) cc_final: 0.4076 (mmm) REVERT: H 90 MET cc_start: 0.7111 (tpp) cc_final: 0.6676 (tpt) REVERT: I 107 LEU cc_start: 0.5194 (OUTLIER) cc_final: 0.4992 (tt) REVERT: J 88 ARG cc_start: 0.5307 (ptm-80) cc_final: 0.5105 (ptm-80) REVERT: J 105 ARG cc_start: 0.4863 (mtt180) cc_final: 0.4466 (mmt-90) REVERT: J 109 LEU cc_start: 0.5847 (tp) cc_final: 0.5557 (mt) REVERT: J 121 LEU cc_start: 0.4880 (mt) cc_final: 0.4172 (mm) REVERT: L 61 GLU cc_start: 0.3576 (OUTLIER) cc_final: 0.2739 (pt0) REVERT: L 74 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.5844 (mm110) REVERT: L 76 ARG cc_start: 0.6875 (mtp85) cc_final: 0.6589 (mtt180) REVERT: L 81 GLU cc_start: 0.6935 (tm-30) cc_final: 0.5997 (tp30) REVERT: L 84 ARG cc_start: 0.6239 (ttm-80) cc_final: 0.5851 (ttm170) REVERT: L 145 GLU cc_start: 0.5361 (mt-10) cc_final: 0.4888 (tt0) REVERT: L 160 LYS cc_start: 0.7507 (mttp) cc_final: 0.6653 (mmtm) REVERT: L 162 GLN cc_start: 0.7653 (pt0) cc_final: 0.6725 (pt0) outliers start: 117 outliers final: 62 residues processed: 479 average time/residue: 0.8800 time to fit residues: 475.9683 Evaluate side-chains 496 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 394 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 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 A residue 536 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 17 LYS 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 97 LYS 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 154 ARG 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 532 ARG 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 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 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 62 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 106 ILE 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 42 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 194 MET 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 86 LYS Chi-restraints excluded: chain F residue 106 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 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 I residue 107 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 151 optimal weight: 10.0000 chunk 364 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 317 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.139834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102679 restraints weight = 32770.501| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.47 r_work: 0.2851 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3588 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= 0.220 Angle : 0.616 11.636 40670 Z= 0.318 Chirality : 0.047 0.195 4560 Planarity : 0.006 0.059 5330 Dihedral : 4.935 66.102 4185 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.72 % Rotamer: Outliers : 3.60 % Allowed : 18.13 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.14), residues: 3764 helix: 1.60 (0.13), residues: 1565 sheet: -0.26 (0.21), residues: 581 loop : 0.11 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 481 TYR 0.016 0.002 TYR A 25 PHE 0.019 0.002 PHE A 574 TRP 0.011 0.002 TRP C 187 HIS 0.004 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00537 (30023) covalent geometry : angle 0.61556 (40670) hydrogen bonds : bond 0.05129 ( 1332) hydrogen bonds : angle 4.71981 ( 3807) ********************** 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 511 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 400 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7577 (mmm) REVERT: A 29 LYS cc_start: 0.8409 (mttt) cc_final: 0.8154 (mtpp) REVERT: A 53 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: A 109 HIS cc_start: 0.7877 (m-70) cc_final: 0.7553 (m170) REVERT: A 156 ARG cc_start: 0.6617 (ttp80) cc_final: 0.6252 (ttp80) REVERT: A 340 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7408 (mpt-90) REVERT: A 449 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 469 GLN cc_start: 0.7525 (mt0) cc_final: 0.7050 (mm110) REVERT: B 19 MET cc_start: 0.8842 (mmm) cc_final: 0.8424 (mmm) REVERT: B 32 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: B 93 ARG cc_start: 0.7553 (mtp180) cc_final: 0.7284 (mmm160) REVERT: B 122 MET cc_start: 0.8139 (mtm) cc_final: 0.7934 (mtt) REVERT: B 124 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6946 (mppt) REVERT: B 130 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7162 (ptm-80) REVERT: B 154 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6920 (ptp90) REVERT: B 276 LYS cc_start: 0.7479 (mmtt) cc_final: 0.6891 (ptmt) REVERT: B 391 MET cc_start: 0.7520 (mmp) cc_final: 0.7294 (mmt) REVERT: B 410 ASP cc_start: 0.8594 (p0) cc_final: 0.8273 (p0) REVERT: B 467 ILE cc_start: 0.7544 (mt) cc_final: 0.7236 (tp) REVERT: B 509 MET cc_start: 0.8953 (mmm) cc_final: 0.8556 (mmm) REVERT: B 524 LYS cc_start: 0.7730 (tttt) cc_final: 0.7260 (mppt) REVERT: C 29 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8684 (mmtp) REVERT: C 156 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.7066 (mmm-85) REVERT: C 180 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6758 (mm-30) REVERT: C 191 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8173 (mtm180) REVERT: C 336 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: C 342 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: C 467 ILE cc_start: 0.7221 (mt) cc_final: 0.7009 (mm) REVERT: C 480 GLU cc_start: 0.7493 (mp0) cc_final: 0.6926 (mp0) REVERT: C 547 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6881 (tpt90) REVERT: D 52 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: D 98 LYS cc_start: 0.7922 (tttt) cc_final: 0.7442 (mmmm) REVERT: D 106 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7871 (pt) REVERT: D 162 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: D 236 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8475 (mtt90) REVERT: D 248 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7555 (mm-30) REVERT: D 280 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7852 (ttp-110) REVERT: D 398 ILE cc_start: 0.8312 (mt) cc_final: 0.8022 (mm) REVERT: D 413 GLN cc_start: 0.8101 (mt0) cc_final: 0.7852 (mt0) REVERT: D 420 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7478 (mmt-90) REVERT: D 457 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: E 26 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: E 36 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8063 (tttp) REVERT: E 61 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6980 (pt0) REVERT: E 98 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7747 (mmtp) REVERT: E 103 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7873 (mp) REVERT: E 200 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8161 (mt-10) REVERT: E 207 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: E 211 THR cc_start: 0.8560 (p) cc_final: 0.8301 (m) REVERT: E 216 ARG cc_start: 0.8413 (ptt90) cc_final: 0.7979 (ptt-90) REVERT: E 274 ARG cc_start: 0.7969 (mtp180) cc_final: 0.6896 (mmp-170) REVERT: E 376 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7358 (tmtm) REVERT: E 388 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8217 (t0) REVERT: E 452 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7590 (mmtp) REVERT: F 25 LYS cc_start: 0.7100 (ptmm) cc_final: 0.6818 (mtpt) REVERT: F 53 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7653 (mm-30) REVERT: F 79 VAL cc_start: 0.8745 (p) cc_final: 0.8243 (t) REVERT: F 98 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7965 (mmtp) REVERT: F 125 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7336 (ttm170) REVERT: F 210 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7853 (ttt-90) REVERT: F 265 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7837 (tm-30) REVERT: F 373 GLU cc_start: 0.7633 (mp0) cc_final: 0.7248 (pm20) REVERT: F 394 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7656 (mttt) REVERT: G 38 GLU cc_start: 0.8047 (tt0) cc_final: 0.7694 (tp30) REVERT: G 47 MET cc_start: 0.7155 (tpp) cc_final: 0.6837 (tpp) REVERT: G 48 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6222 (mt-10) REVERT: G 139 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5921 (ttm170) REVERT: G 148 LYS cc_start: 0.7598 (mttt) cc_final: 0.7165 (mtpt) REVERT: G 156 LYS cc_start: 0.8470 (mtpp) cc_final: 0.7942 (mttt) REVERT: G 159 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.7874 (mtm110) REVERT: G 166 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: G 198 LYS cc_start: 0.8305 (tttt) cc_final: 0.7423 (mptp) REVERT: H 15 LEU cc_start: 0.5536 (tp) cc_final: 0.5196 (tp) REVERT: H 44 LEU cc_start: 0.6732 (tp) cc_final: 0.6489 (tp) REVERT: H 48 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.4706 (p0) REVERT: H 90 MET cc_start: 0.7139 (tpp) cc_final: 0.6657 (tpp) REVERT: J 105 ARG cc_start: 0.4913 (mtt180) cc_final: 0.4465 (mmt-90) REVERT: J 109 LEU cc_start: 0.5889 (tp) cc_final: 0.5581 (mt) REVERT: J 121 LEU cc_start: 0.4996 (mt) cc_final: 0.4289 (mm) REVERT: L 74 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.5892 (mm-40) REVERT: L 76 ARG cc_start: 0.6916 (mtp85) cc_final: 0.6616 (mtt180) REVERT: L 81 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6002 (tp30) REVERT: L 84 ARG cc_start: 0.6207 (ttm-80) cc_final: 0.5699 (ttt180) REVERT: L 145 GLU cc_start: 0.5341 (mt-10) cc_final: 0.4845 (tt0) REVERT: L 160 LYS cc_start: 0.7556 (mttp) cc_final: 0.6664 (mmtm) REVERT: L 162 GLN cc_start: 0.7688 (pt0) cc_final: 0.7451 (pt0) outliers start: 111 outliers final: 58 residues processed: 472 average time/residue: 0.9597 time to fit residues: 509.1018 Evaluate side-chains 484 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 392 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 432 THR Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 536 ILE 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 40 ILE Chi-restraints excluded: chain B residue 97 LYS 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 154 ARG 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 532 ARG Chi-restraints excluded: chain C residue 29 LYS 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 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 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 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 61 GLU Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 103 LEU 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 23 ASN Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 106 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 103 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 321 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 363 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.139856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.103152 restraints weight = 32838.727| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.53 r_work: 0.2849 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 30023 Z= 0.226 Angle : 0.728 59.199 40670 Z= 0.398 Chirality : 0.047 0.498 4560 Planarity : 0.005 0.059 5330 Dihedral : 4.930 66.056 4185 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Rotamer: Outliers : 3.24 % Allowed : 18.59 % Favored : 78.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.14), residues: 3764 helix: 1.59 (0.13), residues: 1565 sheet: -0.26 (0.21), residues: 581 loop : 0.11 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 481 TYR 0.048 0.002 TYR H 21 PHE 0.018 0.002 PHE A 574 TRP 0.011 0.002 TRP A 119 HIS 0.005 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00534 (30023) covalent geometry : angle 0.72760 (40670) hydrogen bonds : bond 0.05058 ( 1332) hydrogen bonds : angle 4.71831 ( 3807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13299.56 seconds wall clock time: 226 minutes 17.62 seconds (13577.62 seconds total)