Starting phenix.real_space_refine on Tue May 27 12:10:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gxx_34364/05_2025/8gxx_34364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gxx_34364/05_2025/8gxx_34364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gxx_34364/05_2025/8gxx_34364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gxx_34364/05_2025/8gxx_34364.map" model { file = "/net/cci-nas-00/data/ceres_data/8gxx_34364/05_2025/8gxx_34364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gxx_34364/05_2025/8gxx_34364.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29553 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.40, per 1000 atoms: 0.59 Number of scatterers: 29553 At special positions: 0 Unit cell: (148.57, 148.57, 176.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 8 15.00 Mg 2 11.99 O 5574 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.21 Conformation dependent library (CDL) restraints added in 3.6 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 26 sheets defined 48.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.516A pdb=" N ILE A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.890A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.256A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.881A 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: 3.656A 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 431 through 443 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.683A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.557A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 4.088A pdb=" N GLU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.537A 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 577 removed outlier: 4.222A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.708A pdb=" N THR B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.534A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.750A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.610A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 435 through 443 removed outlier: 3.545A pdb=" N TYR B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 removed outlier: 4.476A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.513A pdb=" N GLN B 541 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 551 removed outlier: 4.318A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 576 removed outlier: 4.386A pdb=" N GLU B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 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: 3.889A 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 296 through 316 removed outlier: 4.235A pdb=" N GLU C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.899A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 364 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.518A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 431 through 443 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.979A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 533 Processing helix chain 'C' and resid 535 through 542 removed outlier: 3.770A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.572A pdb=" N LYS C 568 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.605A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.797A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 249 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 removed outlier: 3.770A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) 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 366 removed outlier: 3.717A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.834A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.967A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 4.067A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 228 through 250 removed outlier: 3.653A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.711A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 347 Processing helix chain 'E' and resid 361 through 365 removed outlier: 3.556A pdb=" N ASN E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.521A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.536A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 445 through 446 No H-bonds generated for 'chain 'E' and resid 445 through 446' Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.745A pdb=" N LEU E 451 " --> pdb=" O GLN E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 removed outlier: 3.553A pdb=" N ILE E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.800A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 211 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: 3.559A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.338A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' 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 346 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.880A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.727A 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: 3.724A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.736A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 122 through 167 Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.989A pdb=" N ARG H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 54 through 59 Processing helix chain 'H' and resid 59 through 64 removed outlier: 3.614A pdb=" N MET H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.791A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 94 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.693A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 126 No H-bonds generated for 'chain 'J' and resid 124 through 126' Processing helix chain 'J' and resid 127 through 139 removed outlier: 5.175A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.722A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 104 removed outlier: 3.524A pdb=" N ARG K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 127 through 130 removed outlier: 3.514A pdb=" N HIS L 130 " --> pdb=" O ASP L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 130' Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.695A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 187 removed outlier: 4.041A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.178A 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: 6.507A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 6.638A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.980A 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: 5.872A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.704A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.876A 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: 6.572A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (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: 6.041A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.562A 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: 6.141A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.566A 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 164 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 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 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: 3.705A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.770A 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: 6.788A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 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 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.973A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.636A pdb=" N GLY B 155 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.828A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.594A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.745A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.588A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.475A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.859A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR E 258 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA E 192 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.640A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 313 through 315 removed outlier: 9.717A pdb=" N GLN E 336 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N LEU E 355 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN E 338 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.526A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.509A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.655A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 96 Processing sheet with id=AC8, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.305A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1339 hydrogen bonds defined for protein. 3822 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: 10.34 Time building geometry restraints manager: 8.21 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: 9965 1.34 - 1.46: 4291 1.46 - 1.57: 15651 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30110 Sorted by residual: bond pdb=" CA GLU D 296 " pdb=" C GLU D 296 " ideal model delta sigma weight residual 1.522 1.475 0.046 1.72e-02 3.38e+03 7.31e+00 bond pdb=" C MET D 445 " pdb=" N LEU D 446 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.83e-02 1.25e+03 5.96e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 39801 1.43 - 2.85: 769 2.85 - 4.28: 197 4.28 - 5.71: 31 5.71 - 7.13: 9 Bond angle restraints: 40807 Sorted by residual: angle pdb=" N ILE A 40 " pdb=" CA ILE A 40 " pdb=" C ILE A 40 " ideal model delta sigma weight residual 113.20 110.29 2.91 9.60e-01 1.09e+00 9.19e+00 angle pdb=" C3' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" C5' ATP B 601 " ideal model delta sigma weight residual 115.19 110.11 5.08 1.76e+00 3.23e-01 8.32e+00 angle pdb=" N PRO A 420 " pdb=" CA PRO A 420 " pdb=" C PRO A 420 " ideal model delta sigma weight residual 112.10 119.23 -7.13 2.60e+00 1.48e-01 7.53e+00 angle pdb=" C3' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O4' ATP C 601 " ideal model delta sigma weight residual 105.22 101.88 3.34 1.30e+00 5.94e-01 6.62e+00 angle pdb=" C PHE B 141 " pdb=" CA PHE B 141 " pdb=" CB PHE B 141 " ideal model delta sigma weight residual 110.42 115.52 -5.10 1.99e+00 2.53e-01 6.57e+00 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 18054 31.32 - 62.64: 296 62.64 - 93.96: 32 93.96 - 125.28: 0 125.28 - 156.60: 1 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 96.60 -156.60 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" CA LEU A 181 " pdb=" C LEU A 181 " pdb=" N LYS A 182 " pdb=" CA LYS A 182 " ideal model delta harmonic sigma weight residual -180.00 -155.70 -24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual -180.00 -157.60 -22.40 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3777 0.057 - 0.114: 721 0.114 - 0.171: 67 0.171 - 0.228: 1 0.228 - 0.285: 6 Chirality restraints: 4572 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' ATP C 601 " pdb=" C2' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O3' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 200 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 201 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 446 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO F 447 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 447 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 447 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 542 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 543 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.027 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 68 2.39 - 3.01: 18291 3.01 - 3.64: 43518 3.64 - 4.27: 68760 4.27 - 4.90: 116289 Nonbonded interactions: 246926 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.758 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.782 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 1.928 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 1.955 3.040 nonbonded pdb=" O LYS D 370 " pdb=" OG1 THR D 371 " model vdw 1.980 3.040 ... (remaining 246921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 8.020 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: 0.000 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 62.520 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.006 0.069 30110 Z= 0.267 Angle : 0.557 7.133 40807 Z= 0.292 Chirality : 0.045 0.285 4572 Planarity : 0.005 0.054 5333 Dihedral : 11.837 156.600 11465 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3764 helix: 1.51 (0.13), residues: 1546 sheet: -0.75 (0.21), residues: 611 loop : -0.02 (0.17), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 175 HIS 0.005 0.001 HIS B 145 PHE 0.016 0.002 PHE A 230 TYR 0.016 0.002 TYR B 428 ARG 0.009 0.001 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.14526 ( 1339) hydrogen bonds : angle 6.23826 ( 3822) covalent geometry : bond 0.00607 (30110) covalent geometry : angle 0.55704 (40807) *********************** 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 820 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 818 time to evaluate : 3.243 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7128 (ttt-90) REVERT: A 107 VAL cc_start: 0.8510 (t) cc_final: 0.8306 (t) REVERT: A 130 ARG cc_start: 0.7479 (mtm110) cc_final: 0.6953 (ptt-90) REVERT: A 169 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6888 (mt-10) REVERT: A 170 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6643 (mt-10) REVERT: A 179 THR cc_start: 0.8159 (t) cc_final: 0.7491 (p) REVERT: A 343 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 481 ARG cc_start: 0.7367 (mtp85) cc_final: 0.7083 (ttt90) REVERT: A 517 LYS cc_start: 0.7253 (tptp) cc_final: 0.6732 (tttt) REVERT: A 532 ARG cc_start: 0.6815 (ptt90) cc_final: 0.6546 (tmm-80) REVERT: B 3 GLN cc_start: 0.7791 (tt0) cc_final: 0.7247 (mt0) REVERT: B 124 LYS cc_start: 0.7318 (pttm) cc_final: 0.6737 (mptt) REVERT: B 209 MET cc_start: 0.7470 (mtp) cc_final: 0.7244 (mtt) REVERT: B 230 PHE cc_start: 0.5674 (p90) cc_final: 0.5148 (p90) REVERT: B 268 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6840 (tp30) REVERT: B 406 PHE cc_start: 0.7776 (t80) cc_final: 0.7287 (t80) REVERT: B 408 ARG cc_start: 0.7309 (mtp180) cc_final: 0.6971 (ttm-80) REVERT: B 509 MET cc_start: 0.6576 (mmm) cc_final: 0.5522 (tmt) REVERT: B 550 ARG cc_start: 0.5560 (mmm160) cc_final: 0.5266 (mmt90) REVERT: C 19 MET cc_start: 0.8986 (mmm) cc_final: 0.8636 (mmm) REVERT: C 93 ARG cc_start: 0.7835 (mmp80) cc_final: 0.7153 (mmm160) REVERT: C 197 ARG cc_start: 0.7419 (ttp80) cc_final: 0.7032 (ptm-80) REVERT: C 336 GLU cc_start: 0.7707 (tp30) cc_final: 0.7427 (mm-30) REVERT: C 347 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7493 (mt-10) REVERT: C 480 GLU cc_start: 0.7426 (mp0) cc_final: 0.7071 (mt-10) REVERT: C 547 ARG cc_start: 0.7364 (ttm110) cc_final: 0.7121 (ttt90) REVERT: C 567 MET cc_start: 0.7209 (mmm) cc_final: 0.6822 (mmm) REVERT: D 9 THR cc_start: 0.8569 (m) cc_final: 0.8358 (p) REVERT: D 49 GLU cc_start: 0.7939 (tt0) cc_final: 0.7532 (OUTLIER) REVERT: D 206 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6710 (pt0) REVERT: D 388 ASN cc_start: 0.7466 (m-40) cc_final: 0.7245 (m-40) REVERT: D 437 GLN cc_start: 0.8151 (tt0) cc_final: 0.7851 (tt0) REVERT: E 15 SER cc_start: 0.8386 (t) cc_final: 0.7876 (p) REVERT: E 77 GLU cc_start: 0.8304 (pt0) cc_final: 0.7986 (pt0) REVERT: E 81 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.7313 (mpt-90) REVERT: E 209 GLU cc_start: 0.7653 (tt0) cc_final: 0.7193 (tp30) REVERT: E 230 GLU cc_start: 0.7948 (tt0) cc_final: 0.7661 (tt0) REVERT: E 345 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.6913 (mtm-85) REVERT: E 362 MET cc_start: 0.8745 (ttp) cc_final: 0.8146 (ttp) REVERT: E 461 LYS cc_start: 0.6741 (mtpt) cc_final: 0.6237 (tttt) REVERT: F 6 LYS cc_start: 0.7288 (ttpp) cc_final: 0.6903 (ptpt) REVERT: F 46 GLN cc_start: 0.9070 (tt0) cc_final: 0.8829 (tt0) REVERT: F 162 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7532 (mp0) REVERT: F 250 ASP cc_start: 0.8251 (m-30) cc_final: 0.8022 (m-30) REVERT: F 305 LYS cc_start: 0.7908 (mttt) cc_final: 0.7077 (mmmt) REVERT: F 373 GLU cc_start: 0.7121 (mp0) cc_final: 0.6835 (pm20) REVERT: G 148 LYS cc_start: 0.6223 (ttmm) cc_final: 0.5782 (tttt) REVERT: I 104 MET cc_start: 0.4639 (mtm) cc_final: 0.4228 (tmm) REVERT: J 67 LEU cc_start: 0.5734 (mt) cc_final: 0.5464 (tp) REVERT: J 113 GLU cc_start: 0.5213 (mt-10) cc_final: 0.4687 (tp30) REVERT: J 164 GLU cc_start: 0.5723 (tp30) cc_final: 0.5490 (tt0) REVERT: L 112 LEU cc_start: 0.6439 (mt) cc_final: 0.6058 (tm) outliers start: 2 outliers final: 2 residues processed: 818 average time/residue: 1.7469 time to fit residues: 1620.3453 Evaluate side-chains 449 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 292 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 397 GLN A 469 GLN B 3 GLN B 7 GLN B 145 HIS B 260 ASN B 290 ASN C 109 HIS C 501 HIS D 161 ASN D 252 HIS D 344 HIS D 375 HIS D 407 ASN E 23 ASN E 363 ASN E 364 ASN E 448 GLN F 23 ASN F 161 ASN F 206 GLN F 363 ASN F 364 ASN F 388 ASN F 407 ASN F 424 ASN F 428 GLN F 448 GLN G 22 GLN G 55 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120737 restraints weight = 37669.453| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.62 r_work: 0.3233 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30110 Z= 0.147 Angle : 0.576 11.720 40807 Z= 0.297 Chirality : 0.044 0.207 4572 Planarity : 0.005 0.068 5333 Dihedral : 6.683 151.745 4261 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.72 % Rotamer: Outliers : 3.76 % Allowed : 12.71 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3764 helix: 1.70 (0.13), residues: 1564 sheet: -0.57 (0.21), residues: 608 loop : 0.12 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 175 HIS 0.005 0.001 HIS C 145 PHE 0.014 0.001 PHE C 559 TYR 0.014 0.001 TYR B 428 ARG 0.007 0.001 ARG C 488 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 1339) hydrogen bonds : angle 5.05527 ( 3822) covalent geometry : bond 0.00341 (30110) covalent geometry : angle 0.57647 (40807) *********************** 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 610 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 494 time to evaluate : 3.383 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7305 (mppt) REVERT: A 130 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7493 (ptt-90) REVERT: A 343 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7600 (mt-10) REVERT: A 456 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: A 481 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6841 (ttp-110) REVERT: A 493 ASP cc_start: 0.7300 (m-30) cc_final: 0.7044 (m-30) REVERT: A 517 LYS cc_start: 0.7510 (tptp) cc_final: 0.7094 (tttt) REVERT: A 524 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7340 (tttt) REVERT: A 532 ARG cc_start: 0.6622 (ptt90) cc_final: 0.6358 (tmm-80) REVERT: B 3 GLN cc_start: 0.8014 (tt0) cc_final: 0.7462 (mt0) REVERT: B 69 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8016 (mt) REVERT: B 124 LYS cc_start: 0.7553 (pttm) cc_final: 0.6929 (mptt) REVERT: B 133 MET cc_start: 0.8032 (mtm) cc_final: 0.7795 (mtp) REVERT: B 230 PHE cc_start: 0.5776 (p90) cc_final: 0.5265 (p90) REVERT: B 246 ASN cc_start: 0.6969 (t0) cc_final: 0.6762 (t0) REVERT: B 268 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7006 (tp30) REVERT: B 401 ARG cc_start: 0.7092 (mtp85) cc_final: 0.6726 (mtt-85) REVERT: B 408 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7216 (ttm-80) REVERT: B 454 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 509 MET cc_start: 0.6577 (mmm) cc_final: 0.5493 (tmt) REVERT: C 96 GLU cc_start: 0.7706 (pp20) cc_final: 0.7410 (pt0) REVERT: C 124 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7548 (mppt) REVERT: C 197 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7503 (ptm-80) REVERT: C 300 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: C 336 GLU cc_start: 0.7965 (tp30) cc_final: 0.7583 (mm-30) REVERT: C 480 GLU cc_start: 0.7655 (mp0) cc_final: 0.7170 (mt-10) REVERT: C 542 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7620 (mp) REVERT: C 547 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7342 (ttt90) REVERT: C 567 MET cc_start: 0.7315 (mmm) cc_final: 0.6904 (mmm) REVERT: D 206 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7197 (pt0) REVERT: D 331 TYR cc_start: 0.8187 (m-10) cc_final: 0.7951 (m-10) REVERT: D 388 ASN cc_start: 0.7504 (m-40) cc_final: 0.7265 (m-40) REVERT: D 401 GLU cc_start: 0.6164 (mp0) cc_final: 0.5631 (pm20) REVERT: E 81 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7479 (mpt-90) REVERT: E 209 GLU cc_start: 0.7834 (tt0) cc_final: 0.7327 (tp30) REVERT: E 336 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: E 345 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.6919 (mtm-85) REVERT: F 6 LYS cc_start: 0.7403 (ttpp) cc_final: 0.7062 (ptpt) REVERT: F 9 THR cc_start: 0.7938 (m) cc_final: 0.7447 (p) REVERT: F 46 GLN cc_start: 0.9209 (tt0) cc_final: 0.9007 (tt0) REVERT: F 305 LYS cc_start: 0.8029 (mttt) cc_final: 0.7381 (mmmt) REVERT: F 345 ARG cc_start: 0.7984 (mmt90) cc_final: 0.7715 (mtt180) REVERT: F 453 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8106 (mtt180) REVERT: G 159 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6681 (mtt90) REVERT: G 181 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: G 200 LYS cc_start: 0.7096 (mmmt) cc_final: 0.6621 (mmtt) REVERT: I 104 MET cc_start: 0.4798 (mtm) cc_final: 0.4347 (tmm) REVERT: J 66 LEU cc_start: 0.5006 (mt) cc_final: 0.4593 (pt) REVERT: J 89 GLU cc_start: 0.4296 (OUTLIER) cc_final: 0.4066 (mp0) REVERT: J 113 GLU cc_start: 0.5017 (mt-10) cc_final: 0.4715 (tp30) REVERT: J 164 GLU cc_start: 0.6196 (tp30) cc_final: 0.5602 (tt0) REVERT: L 89 GLU cc_start: 0.6438 (pp20) cc_final: 0.6173 (pp20) REVERT: L 102 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.5017 (mm-30) REVERT: L 149 ARG cc_start: 0.6446 (pmt170) cc_final: 0.6152 (ttm170) outliers start: 116 outliers final: 37 residues processed: 556 average time/residue: 1.6172 time to fit residues: 1033.8865 Evaluate side-chains 448 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 400 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 350 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 318 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 240 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN C 109 HIS C 541 GLN D 46 GLN D 407 ASN E 23 ASN E 338 GLN E 363 ASN E 448 GLN F 23 ASN F 206 GLN F 388 ASN G 22 GLN L 130 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.122168 restraints weight = 37463.516| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.76 r_work: 0.3175 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30110 Z= 0.214 Angle : 0.626 9.604 40807 Z= 0.319 Chirality : 0.047 0.193 4572 Planarity : 0.006 0.072 5333 Dihedral : 6.769 133.923 4259 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 4.77 % Allowed : 14.95 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3764 helix: 1.38 (0.13), residues: 1577 sheet: -0.62 (0.21), residues: 618 loop : -0.05 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 100 HIS 0.007 0.001 HIS D 375 PHE 0.015 0.002 PHE C 230 TYR 0.026 0.002 TYR B 428 ARG 0.007 0.001 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 1339) hydrogen bonds : angle 4.96324 ( 3822) covalent geometry : bond 0.00522 (30110) covalent geometry : angle 0.62633 (40807) *********************** 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 556 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 409 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: A 98 THR cc_start: 0.8079 (m) cc_final: 0.7768 (p) REVERT: A 104 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6408 (mtp85) REVERT: A 124 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7433 (mppt) REVERT: A 130 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7462 (ptt-90) REVERT: A 158 LYS cc_start: 0.7740 (tttt) cc_final: 0.7513 (ttmm) REVERT: A 410 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: A 481 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7080 (ttm110) REVERT: A 493 ASP cc_start: 0.7486 (m-30) cc_final: 0.7235 (m-30) REVERT: A 517 LYS cc_start: 0.7525 (tptp) cc_final: 0.7249 (tttt) REVERT: A 532 ARG cc_start: 0.6723 (ptt90) cc_final: 0.6182 (ptt-90) REVERT: B 69 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7881 (mt) REVERT: B 122 MET cc_start: 0.7228 (mtt) cc_final: 0.6911 (mtp) REVERT: B 246 ASN cc_start: 0.7108 (t0) cc_final: 0.6769 (t0) REVERT: B 268 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7060 (mm-30) REVERT: B 401 ARG cc_start: 0.7319 (mtp85) cc_final: 0.6898 (mtt-85) REVERT: B 454 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8151 (mp) REVERT: B 509 MET cc_start: 0.6638 (mmm) cc_final: 0.5855 (tmm) REVERT: B 550 ARG cc_start: 0.5568 (mmm160) cc_final: 0.5334 (tpt170) REVERT: C 96 GLU cc_start: 0.7736 (pp20) cc_final: 0.7390 (pt0) REVERT: C 137 THR cc_start: 0.8802 (t) cc_final: 0.8533 (m) REVERT: C 197 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7642 (ptm-80) REVERT: C 300 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: C 336 GLU cc_start: 0.8074 (tp30) cc_final: 0.7670 (mm-30) REVERT: C 542 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7566 (mp) REVERT: C 546 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: C 547 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7495 (ttt90) REVERT: C 550 ARG cc_start: 0.7779 (mmm160) cc_final: 0.7195 (mtt180) REVERT: C 567 MET cc_start: 0.7494 (mmm) cc_final: 0.6902 (mmm) REVERT: D 62 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6165 (mm-30) REVERT: D 126 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7848 (ttpp) REVERT: D 206 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7311 (pt0) REVERT: D 433 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: E 81 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7571 (mpt-90) REVERT: E 109 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: E 209 GLU cc_start: 0.7875 (tt0) cc_final: 0.7447 (tp30) REVERT: E 336 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: E 345 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.6867 (mtm-85) REVERT: E 416 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7232 (t70) REVERT: F 6 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7171 (ptpt) REVERT: F 88 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8742 (mtt) REVERT: F 100 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7568 (pt) REVERT: F 280 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7474 (mtm180) REVERT: F 305 LYS cc_start: 0.8015 (mttt) cc_final: 0.7485 (mmmt) REVERT: F 345 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7836 (mtt180) REVERT: F 442 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8669 (mp) REVERT: F 453 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8500 (mtt180) REVERT: G 13 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8136 (tm-30) REVERT: G 159 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6839 (mtt90) REVERT: G 181 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: G 196 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7581 (mtp-110) REVERT: I 104 MET cc_start: 0.4926 (mtm) cc_final: 0.4167 (tmm) REVERT: J 66 LEU cc_start: 0.5194 (mt) cc_final: 0.4570 (pt) REVERT: J 67 LEU cc_start: 0.5667 (mt) cc_final: 0.5039 (tp) REVERT: J 164 GLU cc_start: 0.6320 (tp30) cc_final: 0.5517 (tt0) REVERT: K 104 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.4382 (mpp) REVERT: L 67 LEU cc_start: 0.5075 (OUTLIER) cc_final: 0.4769 (mm) REVERT: L 102 GLU cc_start: 0.5162 (mm-30) cc_final: 0.4861 (tm-30) REVERT: L 150 LEU cc_start: 0.6767 (mt) cc_final: 0.6549 (mm) outliers start: 147 outliers final: 56 residues processed: 504 average time/residue: 1.6285 time to fit residues: 945.8640 Evaluate side-chains 438 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 360 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 80 optimal weight: 5.9990 chunk 333 optimal weight: 0.7980 chunk 301 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 303 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS D 161 ASN D 407 ASN E 23 ASN E 338 GLN E 363 ASN F 23 ASN F 388 ASN F 407 ASN G 22 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119975 restraints weight = 38250.849| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.67 r_work: 0.3207 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30110 Z= 0.135 Angle : 0.543 8.427 40807 Z= 0.275 Chirality : 0.044 0.158 4572 Planarity : 0.005 0.066 5333 Dihedral : 6.383 112.512 4259 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 3.96 % Allowed : 16.02 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3764 helix: 1.56 (0.13), residues: 1582 sheet: -0.59 (0.21), residues: 603 loop : 0.00 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 100 HIS 0.011 0.001 HIS J 130 PHE 0.013 0.001 PHE C 559 TYR 0.019 0.001 TYR E 13 ARG 0.008 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1339) hydrogen bonds : angle 4.73218 ( 3822) covalent geometry : bond 0.00318 (30110) covalent geometry : angle 0.54342 (40807) *********************** 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 517 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 395 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7677 (p) REVERT: A 104 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.6330 (mtp85) REVERT: A 124 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7346 (mppt) REVERT: A 130 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7380 (ptt-90) REVERT: A 158 LYS cc_start: 0.7571 (tttt) cc_final: 0.7355 (ttmm) REVERT: A 261 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 456 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: A 481 ARG cc_start: 0.7593 (mtp85) cc_final: 0.6982 (ttm110) REVERT: A 517 LYS cc_start: 0.7428 (tptp) cc_final: 0.7129 (tttt) REVERT: A 524 LYS cc_start: 0.7784 (ttpp) cc_final: 0.7317 (tttt) REVERT: B 69 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7937 (mt) REVERT: B 122 MET cc_start: 0.7160 (mtt) cc_final: 0.6845 (mtp) REVERT: B 133 MET cc_start: 0.8075 (mtm) cc_final: 0.7780 (mtp) REVERT: B 246 ASN cc_start: 0.6971 (t0) cc_final: 0.6555 (t0) REVERT: B 268 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6926 (tp30) REVERT: B 401 ARG cc_start: 0.7282 (mtp85) cc_final: 0.6890 (mtt-85) REVERT: B 509 MET cc_start: 0.6386 (mmm) cc_final: 0.5595 (tmm) REVERT: B 520 LEU cc_start: 0.6328 (tt) cc_final: 0.6084 (mt) REVERT: C 96 GLU cc_start: 0.7757 (pp20) cc_final: 0.7375 (pt0) REVERT: C 137 THR cc_start: 0.8736 (t) cc_final: 0.8396 (m) REVERT: C 197 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7660 (ptm-80) REVERT: C 300 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: C 336 GLU cc_start: 0.8060 (tp30) cc_final: 0.7613 (mm-30) REVERT: C 542 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7473 (mp) REVERT: C 546 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6634 (tt0) REVERT: C 547 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7424 (ttt90) REVERT: C 567 MET cc_start: 0.7479 (mmm) cc_final: 0.6900 (mmm) REVERT: D 62 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6064 (mm-30) REVERT: D 206 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7191 (pt0) REVERT: D 407 ASN cc_start: 0.6304 (OUTLIER) cc_final: 0.5899 (m110) REVERT: E 81 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7532 (mpt-90) REVERT: E 209 GLU cc_start: 0.7833 (tt0) cc_final: 0.7533 (mm-30) REVERT: E 336 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: E 345 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.6913 (mtm-85) REVERT: E 410 ARG cc_start: 0.6522 (tpp80) cc_final: 0.6145 (mtm110) REVERT: F 6 LYS cc_start: 0.7441 (ttpp) cc_final: 0.7033 (ptpt) REVERT: F 88 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8753 (mtt) REVERT: F 100 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7533 (pt) REVERT: F 305 LYS cc_start: 0.8020 (mttt) cc_final: 0.7437 (mmmt) REVERT: F 345 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7862 (mtt180) REVERT: F 453 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8269 (mtt180) REVERT: G 13 GLN cc_start: 0.8306 (tm-30) cc_final: 0.8072 (tm-30) REVERT: G 181 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: G 200 LYS cc_start: 0.7116 (mmmt) cc_final: 0.6603 (mmtt) REVERT: I 104 MET cc_start: 0.4688 (mtm) cc_final: 0.4018 (tmm) REVERT: J 66 LEU cc_start: 0.5225 (mt) cc_final: 0.4562 (pp) REVERT: J 67 LEU cc_start: 0.5634 (mt) cc_final: 0.5053 (tp) REVERT: J 164 GLU cc_start: 0.6284 (tp30) cc_final: 0.5480 (tt0) REVERT: L 67 LEU cc_start: 0.5015 (OUTLIER) cc_final: 0.4760 (mm) REVERT: L 102 GLU cc_start: 0.5079 (mm-30) cc_final: 0.4848 (tm-30) outliers start: 122 outliers final: 52 residues processed: 482 average time/residue: 1.5440 time to fit residues: 860.7082 Evaluate side-chains 421 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 354 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 164 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 167 optimal weight: 0.3980 chunk 152 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 357 optimal weight: 7.9990 chunk 354 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS E 23 ASN E 310 GLN E 338 GLN G 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117717 restraints weight = 38163.907| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.67 r_work: 0.3200 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30110 Z= 0.150 Angle : 0.555 8.613 40807 Z= 0.280 Chirality : 0.044 0.166 4572 Planarity : 0.005 0.080 5333 Dihedral : 6.321 99.696 4259 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 4.48 % Allowed : 16.87 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3764 helix: 1.59 (0.13), residues: 1581 sheet: -0.65 (0.21), residues: 616 loop : 0.03 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 100 HIS 0.004 0.001 HIS B 145 PHE 0.014 0.001 PHE C 559 TYR 0.018 0.001 TYR A 439 ARG 0.009 0.000 ARG B 451 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 1339) hydrogen bonds : angle 4.66795 ( 3822) covalent geometry : bond 0.00360 (30110) covalent geometry : angle 0.55458 (40807) *********************** 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 500 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 362 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: A 92 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: A 98 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 104 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.6264 (mtp85) REVERT: A 124 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7336 (mppt) REVERT: A 130 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7377 (ptt-90) REVERT: A 154 ARG cc_start: 0.7399 (ptm160) cc_final: 0.6847 (ptp90) REVERT: A 261 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8324 (mm-30) REVERT: A 344 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8398 (mmm) REVERT: A 410 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: A 456 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: A 481 ARG cc_start: 0.7638 (mtp85) cc_final: 0.7018 (ttm110) REVERT: A 492 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7709 (mt-10) REVERT: A 517 LYS cc_start: 0.7422 (tptp) cc_final: 0.7128 (tttt) REVERT: A 524 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7355 (tttt) REVERT: B 69 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7928 (mt) REVERT: B 122 MET cc_start: 0.7274 (mtt) cc_final: 0.6955 (mtp) REVERT: B 211 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7821 (tp) REVERT: B 246 ASN cc_start: 0.6932 (t0) cc_final: 0.6522 (t0) REVERT: B 268 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6923 (tp30) REVERT: B 401 ARG cc_start: 0.7357 (mtp85) cc_final: 0.6915 (mtt-85) REVERT: B 509 MET cc_start: 0.6497 (mmm) cc_final: 0.5707 (tmm) REVERT: C 96 GLU cc_start: 0.7762 (pp20) cc_final: 0.7391 (pt0) REVERT: C 137 THR cc_start: 0.8776 (t) cc_final: 0.8436 (m) REVERT: C 197 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7649 (ptm-80) REVERT: C 300 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: C 336 GLU cc_start: 0.8093 (tp30) cc_final: 0.7648 (mm-30) REVERT: C 464 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7601 (mt) REVERT: C 542 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7438 (mp) REVERT: C 546 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6416 (tt0) REVERT: C 547 ARG cc_start: 0.7942 (ttm110) cc_final: 0.7492 (ttt90) REVERT: C 550 ARG cc_start: 0.7630 (mmm160) cc_final: 0.7033 (mtt180) REVERT: C 567 MET cc_start: 0.7463 (mmm) cc_final: 0.6863 (mmm) REVERT: D 62 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5999 (mm-30) REVERT: D 206 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7159 (pt0) REVERT: D 466 LYS cc_start: 0.7433 (mmmt) cc_final: 0.6155 (mppt) REVERT: E 81 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7532 (mpt-90) REVERT: E 109 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6860 (tp30) REVERT: E 209 GLU cc_start: 0.7872 (tt0) cc_final: 0.7579 (mm-30) REVERT: E 336 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: E 345 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6941 (mtm-85) REVERT: E 410 ARG cc_start: 0.6571 (tpp80) cc_final: 0.6220 (mtm110) REVERT: E 416 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7173 (t70) REVERT: F 6 LYS cc_start: 0.7496 (ttpp) cc_final: 0.7071 (ptpt) REVERT: F 88 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8785 (mtt) REVERT: F 100 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7446 (pt) REVERT: F 305 LYS cc_start: 0.8032 (mttt) cc_final: 0.7458 (mmmt) REVERT: F 388 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7189 (m110) REVERT: F 453 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8252 (mtt180) REVERT: G 13 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8067 (tm-30) REVERT: G 181 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: I 104 MET cc_start: 0.4789 (mtm) cc_final: 0.4067 (tmm) REVERT: J 66 LEU cc_start: 0.5221 (mt) cc_final: 0.4784 (tp) REVERT: J 67 LEU cc_start: 0.5789 (mt) cc_final: 0.5155 (tp) REVERT: K 104 MET cc_start: 0.5192 (OUTLIER) cc_final: 0.3738 (mpp) REVERT: L 67 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4755 (mm) REVERT: L 150 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5934 (mm) outliers start: 138 outliers final: 60 residues processed: 457 average time/residue: 1.5671 time to fit residues: 830.5653 Evaluate side-chains 432 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 347 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 150 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 137 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 273 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 232 optimal weight: 0.0670 chunk 77 optimal weight: 0.2980 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN C 109 HIS E 23 ASN F 23 ASN F 166 GLN G 22 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.151960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117375 restraints weight = 38369.203| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.72 r_work: 0.3187 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30110 Z= 0.138 Angle : 0.546 10.384 40807 Z= 0.275 Chirality : 0.044 0.226 4572 Planarity : 0.005 0.082 5333 Dihedral : 6.213 92.247 4259 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 4.15 % Allowed : 17.13 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3764 helix: 1.63 (0.13), residues: 1586 sheet: -0.67 (0.20), residues: 618 loop : 0.07 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 100 HIS 0.005 0.001 HIS B 145 PHE 0.014 0.001 PHE C 559 TYR 0.023 0.001 TYR E 13 ARG 0.011 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1339) hydrogen bonds : angle 4.59828 ( 3822) covalent geometry : bond 0.00330 (30110) covalent geometry : angle 0.54610 (40807) *********************** 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 493 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 365 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: A 92 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: A 98 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7704 (p) REVERT: A 104 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.6271 (mtp85) REVERT: A 124 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7322 (mppt) REVERT: A 130 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7381 (ptt-90) REVERT: A 154 ARG cc_start: 0.7411 (ptm160) cc_final: 0.6846 (ptp90) REVERT: A 261 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8343 (mm-30) REVERT: A 323 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: A 344 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8170 (tpp) REVERT: A 456 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 481 ARG cc_start: 0.7619 (mtp85) cc_final: 0.6978 (ttm110) REVERT: A 493 ASP cc_start: 0.7621 (m-30) cc_final: 0.7363 (m-30) REVERT: A 517 LYS cc_start: 0.7339 (tptp) cc_final: 0.7074 (tttt) REVERT: A 524 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7359 (tttt) REVERT: B 69 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7933 (mt) REVERT: B 92 GLU cc_start: 0.7626 (pt0) cc_final: 0.7408 (pt0) REVERT: B 122 MET cc_start: 0.7279 (mtt) cc_final: 0.6967 (mtp) REVERT: B 211 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 246 ASN cc_start: 0.6928 (t0) cc_final: 0.6563 (t0) REVERT: B 268 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6891 (tp30) REVERT: B 401 ARG cc_start: 0.7404 (mtp85) cc_final: 0.6980 (mtt-85) REVERT: B 509 MET cc_start: 0.6445 (mmm) cc_final: 0.5730 (tmt) REVERT: C 96 GLU cc_start: 0.7753 (pp20) cc_final: 0.7346 (pt0) REVERT: C 137 THR cc_start: 0.8767 (t) cc_final: 0.8404 (m) REVERT: C 197 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7669 (ptm-80) REVERT: C 300 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: C 336 GLU cc_start: 0.8103 (tp30) cc_final: 0.7653 (mm-30) REVERT: C 464 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7504 (mt) REVERT: C 542 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7445 (mp) REVERT: C 546 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6409 (tt0) REVERT: C 547 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7510 (ttt90) REVERT: C 550 ARG cc_start: 0.7613 (mmm160) cc_final: 0.7012 (mtt180) REVERT: C 563 PHE cc_start: 0.8403 (t80) cc_final: 0.8061 (t80) REVERT: C 567 MET cc_start: 0.7453 (mmm) cc_final: 0.6835 (mmm) REVERT: D 62 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6008 (mm-30) REVERT: D 206 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7138 (pt0) REVERT: D 466 LYS cc_start: 0.7488 (mmmt) cc_final: 0.6180 (mppt) REVERT: E 81 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7531 (mpt-90) REVERT: E 209 GLU cc_start: 0.7912 (tt0) cc_final: 0.7638 (mm-30) REVERT: E 336 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: E 345 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6931 (mtm-85) REVERT: E 410 ARG cc_start: 0.6625 (tpp80) cc_final: 0.6294 (mtm110) REVERT: E 416 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7203 (t70) REVERT: F 3 LEU cc_start: 0.6940 (tp) cc_final: 0.6573 (tp) REVERT: F 6 LYS cc_start: 0.7484 (ttpp) cc_final: 0.7034 (ptpt) REVERT: F 88 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8782 (mtt) REVERT: F 100 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7648 (mm) REVERT: F 232 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8401 (mp) REVERT: F 305 LYS cc_start: 0.8059 (mttt) cc_final: 0.7464 (mmmt) REVERT: F 388 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7193 (m110) REVERT: F 453 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8247 (mtt180) REVERT: G 200 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6548 (mmtt) REVERT: I 104 MET cc_start: 0.4763 (mtm) cc_final: 0.4149 (tmm) REVERT: J 66 LEU cc_start: 0.5460 (mt) cc_final: 0.4929 (tp) REVERT: J 67 LEU cc_start: 0.5892 (mt) cc_final: 0.5234 (tp) REVERT: K 104 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.3735 (mpp) REVERT: L 67 LEU cc_start: 0.5120 (OUTLIER) cc_final: 0.4778 (mm) REVERT: L 150 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5953 (mm) outliers start: 128 outliers final: 65 residues processed: 457 average time/residue: 1.5495 time to fit residues: 818.3035 Evaluate side-chains 432 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 343 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 150 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 185 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 317 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 338 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN C 109 HIS E 23 ASN F 142 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120524 restraints weight = 37627.609| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.72 r_work: 0.3174 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30110 Z= 0.181 Angle : 0.591 8.871 40807 Z= 0.298 Chirality : 0.045 0.196 4572 Planarity : 0.005 0.082 5333 Dihedral : 6.345 87.012 4259 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.40 % Rotamer: Outliers : 4.38 % Allowed : 17.81 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3764 helix: 1.43 (0.13), residues: 1585 sheet: -0.72 (0.20), residues: 625 loop : 0.02 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 100 HIS 0.005 0.001 HIS F 344 PHE 0.017 0.002 PHE C 559 TYR 0.022 0.002 TYR A 439 ARG 0.010 0.001 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 1339) hydrogen bonds : angle 4.69214 ( 3822) covalent geometry : bond 0.00439 (30110) covalent geometry : angle 0.59085 (40807) *********************** 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 494 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 359 time to evaluate : 3.137 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: A 92 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: A 104 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.6372 (mtp85) REVERT: A 130 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7340 (ptt-90) REVERT: A 154 ARG cc_start: 0.7430 (ptm160) cc_final: 0.6857 (ptp90) REVERT: A 158 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7347 (mttt) REVERT: A 261 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8405 (mm-30) REVERT: A 323 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8055 (mpp) REVERT: A 344 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8210 (tpp) REVERT: A 481 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7033 (ttm110) REVERT: A 517 LYS cc_start: 0.7379 (tptp) cc_final: 0.7126 (tttt) REVERT: A 524 LYS cc_start: 0.7802 (ttpp) cc_final: 0.7350 (tttt) REVERT: B 69 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7924 (mt) REVERT: B 122 MET cc_start: 0.7392 (mtt) cc_final: 0.7067 (mtp) REVERT: B 210 ARG cc_start: 0.6859 (mtm-85) cc_final: 0.6619 (mtt90) REVERT: B 211 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7856 (tp) REVERT: B 246 ASN cc_start: 0.6839 (t0) cc_final: 0.6502 (t0) REVERT: B 268 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6960 (tp30) REVERT: B 401 ARG cc_start: 0.7395 (mtp85) cc_final: 0.6992 (mtt-85) REVERT: B 488 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.5659 (ptm160) REVERT: B 509 MET cc_start: 0.6544 (mmm) cc_final: 0.5811 (tmt) REVERT: B 550 ARG cc_start: 0.5598 (mmm160) cc_final: 0.5128 (tpm170) REVERT: C 96 GLU cc_start: 0.7741 (pp20) cc_final: 0.7358 (pt0) REVERT: C 130 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7618 (mtp180) REVERT: C 137 THR cc_start: 0.8772 (t) cc_final: 0.8396 (m) REVERT: C 197 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7652 (ptm-80) REVERT: C 276 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6682 (ptpt) REVERT: C 300 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: C 336 GLU cc_start: 0.8187 (tp30) cc_final: 0.7739 (mm-30) REVERT: C 542 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7408 (mp) REVERT: C 546 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6716 (tt0) REVERT: C 547 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7456 (ttt90) REVERT: C 563 PHE cc_start: 0.8446 (t80) cc_final: 0.8191 (t80) REVERT: C 567 MET cc_start: 0.7484 (mmm) cc_final: 0.6858 (mmm) REVERT: D 62 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6058 (mm-30) REVERT: D 206 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7201 (pt0) REVERT: D 466 LYS cc_start: 0.7481 (mmmt) cc_final: 0.6183 (mppt) REVERT: E 81 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7537 (mpt-90) REVERT: E 209 GLU cc_start: 0.7969 (tt0) cc_final: 0.7679 (mm-30) REVERT: E 336 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: E 345 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.6840 (mtm-85) REVERT: E 410 ARG cc_start: 0.6738 (tpp80) cc_final: 0.6329 (mtm110) REVERT: E 416 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7311 (t70) REVERT: F 3 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6549 (tp) REVERT: F 6 LYS cc_start: 0.7515 (ttpp) cc_final: 0.7085 (ptpt) REVERT: F 53 GLU cc_start: 0.7897 (mp0) cc_final: 0.7516 (mp0) REVERT: F 232 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8372 (mp) REVERT: F 305 LYS cc_start: 0.8104 (mttt) cc_final: 0.7550 (mmmt) REVERT: F 388 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7259 (m110) REVERT: G 13 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8145 (tm-30) REVERT: H 103 LYS cc_start: 0.6192 (ttmt) cc_final: 0.5834 (tmmm) REVERT: I 104 MET cc_start: 0.4740 (mtm) cc_final: 0.4170 (tmm) REVERT: J 66 LEU cc_start: 0.5408 (mt) cc_final: 0.4918 (tp) REVERT: J 67 LEU cc_start: 0.5783 (mt) cc_final: 0.5140 (tp) REVERT: J 119 LYS cc_start: 0.6431 (tttt) cc_final: 0.5468 (pptt) REVERT: K 104 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.3689 (mpp) REVERT: L 67 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4680 (mm) outliers start: 135 outliers final: 69 residues processed: 451 average time/residue: 1.5831 time to fit residues: 827.5134 Evaluate side-chains 432 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 343 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 170 optimal weight: 3.9990 chunk 252 optimal weight: 0.2980 chunk 222 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 206 optimal weight: 0.0470 chunk 131 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS E 23 ASN F 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.158503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124246 restraints weight = 37766.254| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.63 r_work: 0.3219 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 30110 Z= 0.108 Angle : 0.520 9.141 40807 Z= 0.260 Chirality : 0.043 0.192 4572 Planarity : 0.005 0.084 5333 Dihedral : 5.991 83.363 4259 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.76 % Allowed : 19.40 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3764 helix: 1.71 (0.13), residues: 1593 sheet: -0.64 (0.21), residues: 599 loop : 0.11 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 100 HIS 0.005 0.001 HIS B 145 PHE 0.014 0.001 PHE E 130 TYR 0.018 0.001 TYR E 13 ARG 0.013 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 1339) hydrogen bonds : angle 4.48577 ( 3822) covalent geometry : bond 0.00250 (30110) covalent geometry : angle 0.51958 (40807) *********************** 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 463 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 378 time to evaluate : 3.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7766 (t70) cc_final: 0.7170 (t70) REVERT: A 104 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.6243 (mtp85) REVERT: A 130 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7329 (ptt-90) REVERT: A 154 ARG cc_start: 0.7394 (ptm160) cc_final: 0.6846 (ptp90) REVERT: A 323 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8084 (mpp) REVERT: A 481 ARG cc_start: 0.7590 (mtp85) cc_final: 0.6944 (ttm110) REVERT: A 524 LYS cc_start: 0.7801 (ttpp) cc_final: 0.7369 (tttt) REVERT: A 532 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6796 (ttm110) REVERT: A 547 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6610 (mmm160) REVERT: A 550 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.5962 (mtt180) REVERT: B 122 MET cc_start: 0.7330 (mtt) cc_final: 0.7022 (mtp) REVERT: B 210 ARG cc_start: 0.6784 (mtm-85) cc_final: 0.6571 (mtt90) REVERT: B 211 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7780 (tp) REVERT: B 246 ASN cc_start: 0.6920 (t0) cc_final: 0.6641 (t0) REVERT: B 268 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7007 (tp30) REVERT: B 401 ARG cc_start: 0.7354 (mtp85) cc_final: 0.6981 (mtt-85) REVERT: C 96 GLU cc_start: 0.7761 (pp20) cc_final: 0.7340 (pt0) REVERT: C 130 ARG cc_start: 0.7880 (mmm160) cc_final: 0.7593 (mtp180) REVERT: C 137 THR cc_start: 0.8768 (t) cc_final: 0.8382 (m) REVERT: C 197 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7640 (ptm-80) REVERT: C 276 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6613 (ptpt) REVERT: C 336 GLU cc_start: 0.8124 (tp30) cc_final: 0.7668 (mm-30) REVERT: C 541 GLN cc_start: 0.6604 (mm-40) cc_final: 0.6304 (pt0) REVERT: C 546 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: C 547 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7474 (ttt90) REVERT: C 550 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7098 (mtt180) REVERT: C 563 PHE cc_start: 0.8383 (t80) cc_final: 0.8055 (t80) REVERT: C 567 MET cc_start: 0.7439 (mmm) cc_final: 0.6885 (mmm) REVERT: D 62 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5975 (mm-30) REVERT: D 206 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7264 (pt0) REVERT: D 392 ILE cc_start: 0.8093 (mt) cc_final: 0.7890 (mp) REVERT: D 466 LYS cc_start: 0.7493 (mmmt) cc_final: 0.6190 (mppt) REVERT: E 77 GLU cc_start: 0.8242 (pt0) cc_final: 0.8041 (pt0) REVERT: E 81 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7415 (mpt-90) REVERT: E 345 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.6762 (mtm-85) REVERT: E 410 ARG cc_start: 0.6711 (tpp80) cc_final: 0.6354 (mtm110) REVERT: F 3 LEU cc_start: 0.6852 (tp) cc_final: 0.6522 (tp) REVERT: F 6 LYS cc_start: 0.7412 (ttpp) cc_final: 0.7019 (ptpt) REVERT: F 53 GLU cc_start: 0.7835 (mp0) cc_final: 0.7455 (mp0) REVERT: F 305 LYS cc_start: 0.8076 (mttt) cc_final: 0.7522 (mmmt) REVERT: G 200 LYS cc_start: 0.7015 (mmmt) cc_final: 0.6555 (mmtt) REVERT: H 68 LEU cc_start: 0.4329 (tp) cc_final: 0.3475 (pt) REVERT: H 95 ARG cc_start: 0.5892 (OUTLIER) cc_final: 0.5650 (tmt170) REVERT: H 103 LYS cc_start: 0.6229 (ttmt) cc_final: 0.5837 (tmmm) REVERT: I 104 MET cc_start: 0.4700 (mtm) cc_final: 0.4175 (tmm) REVERT: J 66 LEU cc_start: 0.5444 (mt) cc_final: 0.4930 (tp) REVERT: J 67 LEU cc_start: 0.5836 (mt) cc_final: 0.5202 (tp) REVERT: J 82 GLU cc_start: 0.6722 (mm-30) cc_final: 0.5901 (mm-30) REVERT: L 67 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4529 (mm) outliers start: 85 outliers final: 36 residues processed: 435 average time/residue: 1.5916 time to fit residues: 797.7564 Evaluate side-chains 386 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 339 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 106 optimal weight: 5.9990 chunk 183 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 286 optimal weight: 0.0040 chunk 259 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122055 restraints weight = 37542.144| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.78 r_work: 0.3240 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30110 Z= 0.126 Angle : 0.537 10.142 40807 Z= 0.268 Chirality : 0.043 0.191 4572 Planarity : 0.005 0.083 5333 Dihedral : 5.974 80.486 4259 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.50 % Allowed : 20.18 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1592 sheet: -0.66 (0.20), residues: 614 loop : 0.17 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 100 HIS 0.004 0.001 HIS B 145 PHE 0.014 0.001 PHE C 559 TYR 0.016 0.001 TYR A 439 ARG 0.013 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1339) hydrogen bonds : angle 4.49567 ( 3822) covalent geometry : bond 0.00301 (30110) covalent geometry : angle 0.53657 (40807) *********************** 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 426 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 349 time to evaluate : 3.302 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7796 (t70) cc_final: 0.7185 (t70) REVERT: A 104 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6248 (mtp85) REVERT: A 130 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7350 (ptt-90) REVERT: A 154 ARG cc_start: 0.7411 (ptm160) cc_final: 0.6870 (ptp90) REVERT: A 261 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 481 ARG cc_start: 0.7605 (mtp85) cc_final: 0.6836 (ttp-110) REVERT: A 524 LYS cc_start: 0.7796 (ttpp) cc_final: 0.7372 (tttt) REVERT: A 532 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6773 (ttm110) REVERT: A 547 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6596 (mmm160) REVERT: B 122 MET cc_start: 0.7351 (mtt) cc_final: 0.7044 (mtp) REVERT: B 210 ARG cc_start: 0.6814 (mtm-85) cc_final: 0.6595 (mtt90) REVERT: B 211 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7767 (tp) REVERT: B 246 ASN cc_start: 0.6816 (t0) cc_final: 0.6591 (t0) REVERT: B 268 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6987 (tp30) REVERT: B 401 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6967 (mtt-85) REVERT: C 96 GLU cc_start: 0.7750 (pp20) cc_final: 0.7356 (pt0) REVERT: C 130 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7611 (mtp180) REVERT: C 137 THR cc_start: 0.8784 (t) cc_final: 0.8399 (m) REVERT: C 197 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7647 (ptm-80) REVERT: C 276 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6657 (ptpt) REVERT: C 336 GLU cc_start: 0.8121 (tp30) cc_final: 0.7665 (mm-30) REVERT: C 541 GLN cc_start: 0.6578 (mm-40) cc_final: 0.6301 (pt0) REVERT: C 546 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6504 (tt0) REVERT: C 547 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7480 (ttt90) REVERT: C 550 ARG cc_start: 0.7655 (mmm160) cc_final: 0.7117 (mtt180) REVERT: C 563 PHE cc_start: 0.8374 (t80) cc_final: 0.8056 (t80) REVERT: C 567 MET cc_start: 0.7485 (mmm) cc_final: 0.6916 (mmm) REVERT: D 62 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5924 (mm-30) REVERT: D 206 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7228 (pt0) REVERT: D 392 ILE cc_start: 0.8105 (mt) cc_final: 0.7885 (mp) REVERT: D 466 LYS cc_start: 0.7451 (mmmt) cc_final: 0.6198 (mppt) REVERT: E 77 GLU cc_start: 0.8233 (pt0) cc_final: 0.8016 (pt0) REVERT: E 81 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7387 (mpt-90) REVERT: E 259 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7708 (t0) REVERT: E 345 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.6853 (mtm-85) REVERT: E 410 ARG cc_start: 0.6841 (tpp80) cc_final: 0.6494 (mtm110) REVERT: E 416 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7290 (t70) REVERT: F 3 LEU cc_start: 0.6849 (tp) cc_final: 0.6524 (tp) REVERT: F 6 LYS cc_start: 0.7420 (ttpp) cc_final: 0.7016 (ptpt) REVERT: F 53 GLU cc_start: 0.7819 (mp0) cc_final: 0.7424 (mp0) REVERT: F 305 LYS cc_start: 0.8095 (mttt) cc_final: 0.7516 (mmmt) REVERT: G 200 LYS cc_start: 0.7035 (mmmt) cc_final: 0.6597 (mmtt) REVERT: H 63 MET cc_start: 0.3620 (pmm) cc_final: 0.2408 (mtm) REVERT: H 95 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.5685 (tmt170) REVERT: H 98 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5436 (pp) REVERT: H 103 LYS cc_start: 0.6220 (ttmt) cc_final: 0.5834 (tmmm) REVERT: I 104 MET cc_start: 0.4714 (mtm) cc_final: 0.4183 (tmm) REVERT: J 66 LEU cc_start: 0.5460 (mt) cc_final: 0.4937 (tp) REVERT: J 67 LEU cc_start: 0.5852 (mt) cc_final: 0.5208 (tp) REVERT: J 82 GLU cc_start: 0.6583 (mm-30) cc_final: 0.5923 (mm-30) REVERT: L 67 LEU cc_start: 0.4922 (OUTLIER) cc_final: 0.4534 (mm) outliers start: 77 outliers final: 46 residues processed: 402 average time/residue: 1.6419 time to fit residues: 765.8456 Evaluate side-chains 399 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 341 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 41 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 HIS E 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120072 restraints weight = 37565.203| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.51 r_work: 0.3200 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30110 Z= 0.140 Angle : 0.552 9.628 40807 Z= 0.277 Chirality : 0.044 0.181 4572 Planarity : 0.005 0.084 5333 Dihedral : 6.013 79.590 4259 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.50 % Allowed : 20.34 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3764 helix: 1.66 (0.13), residues: 1593 sheet: -0.68 (0.20), residues: 614 loop : 0.15 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 100 HIS 0.003 0.001 HIS B 145 PHE 0.015 0.001 PHE C 559 TYR 0.023 0.001 TYR E 13 ARG 0.015 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1339) hydrogen bonds : angle 4.53621 ( 3822) covalent geometry : bond 0.00338 (30110) covalent geometry : angle 0.55209 (40807) ********************** 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 421 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 344 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6296 (mtp85) REVERT: A 130 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7305 (ptt-90) REVERT: A 154 ARG cc_start: 0.7392 (ptm160) cc_final: 0.6870 (ptp90) REVERT: A 202 ASN cc_start: 0.8302 (p0) cc_final: 0.7985 (p0) REVERT: A 481 ARG cc_start: 0.7617 (mtp85) cc_final: 0.6824 (ttp-110) REVERT: A 524 LYS cc_start: 0.7796 (ttpp) cc_final: 0.7364 (tttt) REVERT: A 532 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6754 (ttm110) REVERT: B 122 MET cc_start: 0.7416 (mtt) cc_final: 0.7104 (mtp) REVERT: B 211 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7926 (tp) REVERT: B 246 ASN cc_start: 0.6796 (t0) cc_final: 0.6585 (t0) REVERT: B 268 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6959 (tp30) REVERT: B 401 ARG cc_start: 0.7361 (mtp85) cc_final: 0.6947 (mtt-85) REVERT: C 96 GLU cc_start: 0.7777 (pp20) cc_final: 0.7362 (pt0) REVERT: C 137 THR cc_start: 0.8786 (t) cc_final: 0.8393 (m) REVERT: C 197 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7631 (ptm-80) REVERT: C 276 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6667 (ptpt) REVERT: C 336 GLU cc_start: 0.8165 (tp30) cc_final: 0.7718 (mm-30) REVERT: C 546 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6412 (tt0) REVERT: C 547 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7474 (ttt90) REVERT: C 550 ARG cc_start: 0.7700 (mmm160) cc_final: 0.7146 (mtt180) REVERT: C 563 PHE cc_start: 0.8347 (t80) cc_final: 0.8126 (t80) REVERT: C 567 MET cc_start: 0.7424 (mmm) cc_final: 0.6836 (mmm) REVERT: D 62 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5953 (mm-30) REVERT: D 206 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7219 (pt0) REVERT: D 392 ILE cc_start: 0.8115 (mt) cc_final: 0.7900 (mp) REVERT: D 413 GLN cc_start: 0.8087 (mt0) cc_final: 0.7870 (mp10) REVERT: D 466 LYS cc_start: 0.7473 (mmmt) cc_final: 0.6197 (mppt) REVERT: E 77 GLU cc_start: 0.8247 (pt0) cc_final: 0.8033 (pt0) REVERT: E 81 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7612 (mtt90) REVERT: E 259 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7774 (t0) REVERT: E 345 ARG cc_start: 0.7360 (ttm-80) cc_final: 0.6836 (mtm-85) REVERT: E 410 ARG cc_start: 0.6864 (tpp80) cc_final: 0.6440 (mtm110) REVERT: F 3 LEU cc_start: 0.6822 (tp) cc_final: 0.6503 (tp) REVERT: F 6 LYS cc_start: 0.7483 (ttpp) cc_final: 0.7068 (ptpt) REVERT: F 53 GLU cc_start: 0.7872 (mp0) cc_final: 0.7480 (mp0) REVERT: F 305 LYS cc_start: 0.8092 (mttt) cc_final: 0.7529 (mmmt) REVERT: F 442 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8551 (mp) REVERT: G 200 LYS cc_start: 0.6921 (mmmt) cc_final: 0.6492 (mmtt) REVERT: H 68 LEU cc_start: 0.4249 (tp) cc_final: 0.3349 (pt) REVERT: H 95 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5737 (tmt170) REVERT: H 103 LYS cc_start: 0.6229 (ttmt) cc_final: 0.5834 (tmmm) REVERT: I 104 MET cc_start: 0.4673 (mtm) cc_final: 0.4250 (tmm) REVERT: J 66 LEU cc_start: 0.5458 (mt) cc_final: 0.4924 (tp) REVERT: J 67 LEU cc_start: 0.5848 (mt) cc_final: 0.5197 (tp) REVERT: J 82 GLU cc_start: 0.6427 (mm-30) cc_final: 0.5899 (mm-30) REVERT: J 85 ARG cc_start: 0.5080 (ttm110) cc_final: 0.4838 (ptp-110) REVERT: L 67 LEU cc_start: 0.4950 (OUTLIER) cc_final: 0.4546 (mm) outliers start: 77 outliers final: 48 residues processed: 398 average time/residue: 1.5715 time to fit residues: 721.4920 Evaluate side-chains 395 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 279 optimal weight: 0.5980 chunk 323 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 363 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 365 optimal weight: 10.0000 chunk 339 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.155583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118728 restraints weight = 37589.020| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.51 r_work: 0.3184 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30110 Z= 0.159 Angle : 0.571 9.684 40807 Z= 0.287 Chirality : 0.045 0.185 4572 Planarity : 0.005 0.083 5333 Dihedral : 6.111 83.175 4259 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.40 % Allowed : 20.50 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3764 helix: 1.58 (0.13), residues: 1593 sheet: -0.72 (0.20), residues: 614 loop : 0.10 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 100 HIS 0.005 0.001 HIS B 145 PHE 0.016 0.002 PHE C 559 TYR 0.023 0.001 TYR A 439 ARG 0.013 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 1339) hydrogen bonds : angle 4.61543 ( 3822) covalent geometry : bond 0.00384 (30110) covalent geometry : angle 0.57104 (40807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24468.06 seconds wall clock time: 420 minutes 34.46 seconds (25234.46 seconds total)