Starting phenix.real_space_refine on Sun Jul 5 17:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gxx_34364/07_2026/8gxx_34364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gxx_34364/07_2026/8gxx_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8gxx_34364/07_2026/8gxx_34364.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gxx_34364/07_2026/8gxx_34364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gxx_34364/07_2026/8gxx_34364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gxx_34364/07_2026/8gxx_34364.map" model { file = "/net/cci-nas-00/data/ceres_data/8gxx_34364/07_2026/8gxx_34364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gxx_34364/07_2026/8gxx_34364.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 6.94, per 1000 atoms: 0.23 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: 2.92 Conformation dependent library (CDL) restraints added in 1.3 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: 0.93 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: 5.76 Time building geometry restraints manager: 3.84 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: 18019 31.32 - 62.64: 273 62.64 - 93.96: 28 93.96 - 125.28: 0 125.28 - 156.60: 1 Dihedral angle restraints: 18321 sinusoidal: 7499 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 18318 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: 0.000 Normalize map: mean=0, sd=1: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.450 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 11.563 156.600 11403 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 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 ARG 0.009 0.001 ARG D 125 TYR 0.016 0.002 TYR B 428 PHE 0.016 0.002 PHE A 230 TRP 0.008 0.001 TRP J 175 HIS 0.005 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.27 (30110) covalent geometry : angle 0.55704 / 0.29 (40807) hydrogen bonds : bond 0.14526 / 9.74 ( 1339) hydrogen bonds : angle 6.23826 / 4.42 ( 3822) *********************** 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 : 1.187 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: 0.6887 (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: 0.6736 (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: 0.6821 (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: 0.8305 (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: 0.6904 (ptpt) REVERT: F 46 GLN cc_start: 0.9071 (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: 0.6057 (tm) outliers start: 2 outliers final: 2 residues processed: 818 average time/residue: 0.8589 time to fit residues: 798.0154 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 : 1.006 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 397 GLN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 7 GLN B 145 HIS B 260 ASN B 290 ASN C 109 HIS C 501 HIS D 46 GLN 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 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117662 restraints weight = 38057.604| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.76 r_work: 0.3179 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30110 Z= 0.190 Angle : 0.617 12.304 40807 Z= 0.317 Chirality : 0.046 0.216 4572 Planarity : 0.006 0.067 5333 Dihedral : 5.586 143.520 4199 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 4.18 % Allowed : 12.49 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3764 helix: 1.51 (0.13), residues: 1563 sheet: -0.64 (0.21), residues: 626 loop : 0.04 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 156 TYR 0.019 0.002 TYR B 428 PHE 0.016 0.002 PHE C 559 TRP 0.012 0.002 TRP A 119 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (30110) covalent geometry : angle 0.61722 / 0.32 (40807) hydrogen bonds : bond 0.04659 / 3.10 ( 1339) hydrogen bonds : angle 5.08169 / 3.60 ( 3822) *********************** 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 596 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 467 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6228 (mtp85) REVERT: A 124 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7315 (mppt) REVERT: A 130 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7476 (ptt-90) REVERT: A 170 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6909 (mt-10) REVERT: A 343 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 456 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: A 481 ARG cc_start: 0.7540 (mtp85) cc_final: 0.6911 (ttm110) REVERT: A 488 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7720 (ttp80) REVERT: A 517 LYS cc_start: 0.7542 (tptp) cc_final: 0.7124 (tttt) REVERT: A 532 ARG cc_start: 0.6648 (ptt90) cc_final: 0.6121 (ptt-90) REVERT: B 3 GLN cc_start: 0.8045 (tt0) cc_final: 0.7389 (mt0) REVERT: B 69 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7895 (mt) REVERT: B 124 LYS cc_start: 0.7694 (pttm) cc_final: 0.7026 (mptt) REVERT: B 133 MET cc_start: 0.8012 (mtm) cc_final: 0.7765 (mtp) REVERT: B 246 ASN cc_start: 0.7070 (t0) cc_final: 0.6812 (t0) REVERT: B 401 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6809 (mtt-85) REVERT: B 408 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7268 (ttm-80) REVERT: B 454 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8081 (mp) REVERT: B 509 MET cc_start: 0.6652 (mmm) cc_final: 0.5579 (tmt) REVERT: C 85 ASP cc_start: 0.7470 (t0) cc_final: 0.7249 (t0) REVERT: C 93 ARG cc_start: 0.7859 (mmp80) cc_final: 0.7522 (mmm160) REVERT: C 182 LYS cc_start: 0.8509 (mttt) cc_final: 0.8250 (mtmt) REVERT: C 197 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7539 (ptm-80) REVERT: C 300 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: C 336 GLU cc_start: 0.8062 (tp30) cc_final: 0.7678 (mm-30) REVERT: C 347 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 517 LYS cc_start: 0.8150 (tttt) cc_final: 0.7929 (tttp) REVERT: C 542 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7641 (mp) REVERT: C 547 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7365 (ttt90) REVERT: C 567 MET cc_start: 0.7389 (mmm) cc_final: 0.6861 (mmm) REVERT: D 126 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7923 (ttpp) REVERT: D 206 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7178 (pp30) REVERT: D 388 ASN cc_start: 0.7527 (m-40) cc_final: 0.7262 (m-40) REVERT: D 401 GLU cc_start: 0.6220 (mp0) cc_final: 0.5697 (pm20) REVERT: E 77 GLU cc_start: 0.8349 (pt0) cc_final: 0.8140 (pt0) REVERT: E 81 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7492 (mpt-90) REVERT: E 209 GLU cc_start: 0.7911 (tt0) cc_final: 0.7411 (tp30) REVERT: E 336 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: E 338 GLN cc_start: 0.8557 (tt0) cc_final: 0.8336 (tp40) REVERT: E 345 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.6882 (mtm-85) REVERT: E 372 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6773 (mtm-85) REVERT: F 6 LYS cc_start: 0.7495 (ttpp) cc_final: 0.7129 (ptpt) REVERT: F 9 THR cc_start: 0.8063 (m) cc_final: 0.7544 (p) REVERT: F 162 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8130 (mp0) REVERT: F 305 LYS cc_start: 0.8082 (mttt) cc_final: 0.7402 (mmmt) REVERT: F 345 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7835 (mtt180) REVERT: G 13 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8099 (tm-30) REVERT: G 159 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6745 (mtt90) REVERT: G 181 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: G 200 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6664 (mmtt) REVERT: I 104 MET cc_start: 0.4862 (mtm) cc_final: 0.4340 (tmm) REVERT: J 66 LEU cc_start: 0.5138 (mp) cc_final: 0.4703 (pt) REVERT: J 67 LEU cc_start: 0.5631 (mt) cc_final: 0.5367 (tp) REVERT: J 113 GLU cc_start: 0.5196 (mt-10) cc_final: 0.4679 (tp30) REVERT: J 164 GLU cc_start: 0.6162 (tp30) cc_final: 0.5475 (tt0) REVERT: K 104 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.4621 (mpp) REVERT: L 102 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.4951 (tm-30) REVERT: L 160 LYS cc_start: 0.6626 (mmtm) cc_final: 0.6385 (mmtm) outliers start: 129 outliers final: 43 residues processed: 543 average time/residue: 0.7531 time to fit residues: 470.7655 Evaluate side-chains 452 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 395 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 488 ARG 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 206 LEU 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 B residue 454 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 152 ASP 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 50 VAL Chi-restraints excluded: chain D residue 106 ILE 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 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 211 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 372 ARG 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 396 VAL Chi-restraints excluded: chain F residue 457 ASP 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 J residue 128 LEU Chi-restraints excluded: chain K residue 104 MET 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 281 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 270 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 418 HIS C 109 HIS C 541 GLN D 407 ASN E 23 ASN E 310 GLN E 363 ASN E 448 GLN F 23 ASN G 22 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122738 restraints weight = 37683.245| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.72 r_work: 0.3209 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30110 Z= 0.192 Angle : 0.603 9.235 40807 Z= 0.307 Chirality : 0.046 0.199 4572 Planarity : 0.006 0.069 5333 Dihedral : 5.665 123.775 4199 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 4.87 % Allowed : 14.56 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3764 helix: 1.34 (0.13), residues: 1581 sheet: -0.64 (0.21), residues: 613 loop : -0.10 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.024 0.002 TYR B 428 PHE 0.016 0.002 PHE E 421 TRP 0.014 0.002 TRP C 119 HIS 0.005 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (30110) covalent geometry : angle 0.60320 / 0.31 (40807) hydrogen bonds : bond 0.04552 / 3.03 ( 1339) hydrogen bonds : angle 4.93351 / 3.51 ( 3822) *********************** 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 561 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 411 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8059 (m) cc_final: 0.7766 (p) REVERT: A 104 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6498 (mtp85) REVERT: A 124 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7444 (mppt) REVERT: A 130 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7446 (ptt-90) REVERT: A 158 LYS cc_start: 0.7765 (tttt) cc_final: 0.7504 (ttmm) REVERT: A 449 GLU cc_start: 0.8193 (mp0) cc_final: 0.7986 (mp0) REVERT: A 456 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: A 477 GLN cc_start: 0.7939 (mm110) cc_final: 0.7657 (mm-40) REVERT: A 481 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7116 (ttm110) REVERT: A 488 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7815 (ttp80) REVERT: A 517 LYS cc_start: 0.7490 (tptp) cc_final: 0.7221 (tttt) REVERT: A 524 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7422 (tttt) REVERT: A 532 ARG cc_start: 0.6728 (ptt90) cc_final: 0.6150 (ptt-90) REVERT: B 69 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7895 (mt) REVERT: B 122 MET cc_start: 0.7349 (mtt) cc_final: 0.7049 (mtp) REVERT: B 211 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7836 (tp) REVERT: B 246 ASN cc_start: 0.7124 (t0) cc_final: 0.6761 (t0) REVERT: B 268 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6750 (mm-30) REVERT: B 401 ARG cc_start: 0.7244 (mtp85) cc_final: 0.6861 (mtt-85) REVERT: B 454 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 509 MET cc_start: 0.6589 (mmm) cc_final: 0.5837 (tmm) REVERT: C 137 THR cc_start: 0.8780 (t) cc_final: 0.8497 (m) REVERT: C 197 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7697 (ptm-80) REVERT: C 300 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: C 336 GLU cc_start: 0.8051 (tp30) cc_final: 0.7657 (mm-30) REVERT: C 347 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7501 (mt-10) REVERT: C 542 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7545 (mp) REVERT: C 546 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: C 547 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7511 (ttt90) REVERT: C 567 MET cc_start: 0.7511 (mmm) cc_final: 0.6911 (mmm) REVERT: D 62 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6142 (mm-30) REVERT: D 126 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7834 (ttpp) REVERT: D 206 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7318 (pt0) REVERT: D 388 ASN cc_start: 0.7442 (m-40) cc_final: 0.7219 (m-40) REVERT: E 77 GLU cc_start: 0.8338 (pt0) cc_final: 0.8130 (pt0) REVERT: E 81 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7495 (mpt-90) REVERT: E 109 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: E 209 GLU cc_start: 0.7938 (tt0) cc_final: 0.7487 (tp30) REVERT: E 336 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: E 345 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.6861 (mtm-85) REVERT: E 362 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8365 (ttp) REVERT: E 372 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6856 (mtm-85) REVERT: E 410 ARG cc_start: 0.6504 (tpp80) cc_final: 0.6237 (mtm110) REVERT: E 416 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7227 (t70) REVERT: F 6 LYS cc_start: 0.7502 (ttpp) cc_final: 0.7098 (ptpt) REVERT: F 88 MET cc_start: 0.8943 (mtm) cc_final: 0.8737 (mtt) REVERT: F 100 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7462 (pt) REVERT: F 280 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7458 (mtm180) REVERT: F 305 LYS cc_start: 0.8010 (mttt) cc_final: 0.7485 (mmmt) REVERT: F 345 ARG cc_start: 0.8146 (mmt90) cc_final: 0.7892 (mtt180) REVERT: F 388 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7256 (m110) REVERT: G 13 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: G 181 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: G 196 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7473 (mtp-110) REVERT: I 104 MET cc_start: 0.4938 (mtm) cc_final: 0.4146 (tmm) REVERT: J 66 LEU cc_start: 0.5243 (mt) cc_final: 0.4693 (pp) REVERT: J 67 LEU cc_start: 0.5853 (mt) cc_final: 0.5442 (tp) REVERT: J 164 GLU cc_start: 0.6288 (tp30) cc_final: 0.5540 (tt0) REVERT: L 67 LEU cc_start: 0.5042 (OUTLIER) cc_final: 0.4772 (mm) REVERT: L 102 GLU cc_start: 0.5214 (mm-30) cc_final: 0.4999 (tm-30) REVERT: L 150 LEU cc_start: 0.6760 (mt) cc_final: 0.6548 (mm) outliers start: 150 outliers final: 63 residues processed: 509 average time/residue: 0.7938 time to fit residues: 465.6256 Evaluate side-chains 446 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 361 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 488 ARG 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 206 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 268 GLU 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 503 VAL 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 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 445 MET Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 ASP 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 362 MET Chi-restraints excluded: chain E residue 372 ARG 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 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 388 ASN Chi-restraints excluded: chain F residue 396 VAL 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 9 MET Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 43 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 280 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 294 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 260 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS D 161 ASN D 407 ASN E 23 ASN E 363 ASN F 23 ASN F 166 GLN F 388 ASN G 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115788 restraints weight = 38255.272| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.49 r_work: 0.3193 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30110 Z= 0.142 Angle : 0.550 9.995 40807 Z= 0.278 Chirality : 0.044 0.157 4572 Planarity : 0.005 0.055 5333 Dihedral : 5.192 102.277 4197 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 4.38 % Allowed : 16.12 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3764 helix: 1.54 (0.13), residues: 1580 sheet: -0.61 (0.21), residues: 611 loop : -0.04 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 154 TYR 0.021 0.001 TYR E 13 PHE 0.014 0.001 PHE C 559 TRP 0.019 0.001 TRP J 100 HIS 0.009 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (30110) covalent geometry : angle 0.55006 / 0.28 (40807) hydrogen bonds : bond 0.03933 / 2.61 ( 1339) hydrogen bonds : angle 4.73223 / 3.37 ( 3822) *********************** 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 527 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 392 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7821 (t70) cc_final: 0.7180 (t70) REVERT: A 98 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7653 (p) REVERT: A 104 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.6388 (mtp85) REVERT: A 124 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7330 (mppt) REVERT: A 130 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7407 (ptt-90) REVERT: A 154 ARG cc_start: 0.7419 (ptm160) cc_final: 0.6832 (ptp90) REVERT: A 156 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7647 (mtp-110) REVERT: A 158 LYS cc_start: 0.7534 (tttt) cc_final: 0.7321 (ttmm) REVERT: A 456 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: A 481 ARG cc_start: 0.7611 (mtp85) cc_final: 0.6955 (ttm110) REVERT: A 492 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7729 (mt-10) REVERT: A 517 LYS cc_start: 0.7429 (tptp) cc_final: 0.7115 (tttt) REVERT: A 524 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7425 (tttt) REVERT: B 69 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7945 (mt) REVERT: B 122 MET cc_start: 0.7204 (mtt) cc_final: 0.6892 (mtp) REVERT: B 246 ASN cc_start: 0.7000 (t0) cc_final: 0.6580 (t0) REVERT: B 401 ARG cc_start: 0.7292 (mtp85) cc_final: 0.6854 (mtt-85) REVERT: B 509 MET cc_start: 0.6421 (mmm) cc_final: 0.5649 (tmm) REVERT: B 520 LEU cc_start: 0.6362 (tt) cc_final: 0.6123 (mt) REVERT: B 550 ARG cc_start: 0.6356 (tpt170) cc_final: 0.6137 (tpm170) REVERT: C 137 THR cc_start: 0.8778 (t) cc_final: 0.8421 (m) REVERT: C 197 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7620 (ptm-80) REVERT: C 276 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6634 (ptpt) REVERT: C 300 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: C 336 GLU cc_start: 0.8071 (tp30) cc_final: 0.7616 (mm-30) REVERT: C 542 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7444 (mp) REVERT: C 546 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: C 547 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7444 (ttt90) REVERT: C 550 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7067 (mtt180) REVERT: C 567 MET cc_start: 0.7476 (mmm) cc_final: 0.6892 (mmm) REVERT: D 62 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6047 (mm-30) REVERT: D 206 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7157 (pt0) REVERT: D 388 ASN cc_start: 0.7417 (m-40) cc_final: 0.7173 (m-40) REVERT: E 77 GLU cc_start: 0.8288 (pt0) cc_final: 0.8065 (pt0) REVERT: E 81 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7429 (mpt-90) REVERT: E 109 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6875 (tp30) REVERT: E 209 GLU cc_start: 0.7878 (tt0) cc_final: 0.7576 (mm-30) REVERT: E 336 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: E 345 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.6914 (mtm-85) REVERT: E 410 ARG cc_start: 0.6525 (tpp80) cc_final: 0.6159 (mtm110) REVERT: F 6 LYS cc_start: 0.7509 (ttpp) cc_final: 0.7066 (ptpt) REVERT: F 100 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7455 (pt) REVERT: F 305 LYS cc_start: 0.8004 (mttt) cc_final: 0.7418 (mmmt) REVERT: G 13 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: G 181 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: G 200 LYS cc_start: 0.7145 (mmmt) cc_final: 0.6631 (mmtt) REVERT: I 104 MET cc_start: 0.4814 (mtm) cc_final: 0.4116 (tmm) REVERT: J 66 LEU cc_start: 0.5181 (mt) cc_final: 0.4534 (pp) REVERT: J 67 LEU cc_start: 0.5797 (mt) cc_final: 0.5406 (tp) REVERT: K 104 MET cc_start: 0.5368 (OUTLIER) cc_final: 0.4309 (mpp) REVERT: L 67 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4682 (mm) REVERT: L 102 GLU cc_start: 0.5149 (mm-30) cc_final: 0.4917 (tm-30) outliers start: 135 outliers final: 58 residues processed: 483 average time/residue: 0.7082 time to fit residues: 396.4675 Evaluate side-chains 425 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 351 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN 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 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 384 VAL 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 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 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 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 399 ILE 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 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 F residue 5 LYS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 79 VAL 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 442 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 13 GLN 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 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 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 39 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 0.0570 chunk 330 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 230 optimal weight: 0.0000 chunk 7 optimal weight: 2.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS C 541 GLN D 407 ASN E 23 ASN G 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.120153 restraints weight = 38092.791| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.53 r_work: 0.3236 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30110 Z= 0.124 Angle : 0.526 7.813 40807 Z= 0.266 Chirality : 0.043 0.211 4572 Planarity : 0.005 0.044 5333 Dihedral : 5.022 92.717 4197 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 4.28 % Allowed : 17.22 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3764 helix: 1.67 (0.13), residues: 1586 sheet: -0.60 (0.20), residues: 613 loop : 0.05 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 154 TYR 0.016 0.001 TYR A 439 PHE 0.012 0.001 PHE E 421 TRP 0.014 0.001 TRP J 100 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (30110) covalent geometry : angle 0.52625 / 0.27 (40807) hydrogen bonds : bond 0.03680 / 2.44 ( 1339) hydrogen bonds : angle 4.60388 / 3.28 ( 3822) *********************** 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 517 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 385 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7737 (t70) cc_final: 0.7143 (t70) REVERT: A 98 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7681 (p) REVERT: A 104 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6308 (mtp85) REVERT: A 124 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7328 (mppt) REVERT: A 130 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7334 (ptt-90) REVERT: A 154 ARG cc_start: 0.7395 (ptm160) cc_final: 0.6841 (ptp90) REVERT: A 410 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: A 456 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: A 481 ARG cc_start: 0.7587 (mtp85) cc_final: 0.6985 (ttm110) REVERT: A 492 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7463 (mt-10) REVERT: A 493 ASP cc_start: 0.7605 (m-30) cc_final: 0.7352 (m-30) REVERT: A 517 LYS cc_start: 0.7323 (tptp) cc_final: 0.7058 (tttt) REVERT: A 524 LYS cc_start: 0.7846 (ttpp) cc_final: 0.7402 (tttt) REVERT: B 69 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7987 (mt) REVERT: B 122 MET cc_start: 0.7251 (mtt) cc_final: 0.6959 (mtp) REVERT: B 246 ASN cc_start: 0.6883 (t0) cc_final: 0.6503 (t0) REVERT: B 268 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6888 (tp30) REVERT: B 401 ARG cc_start: 0.7271 (mtp85) cc_final: 0.6947 (mtt-85) REVERT: B 509 MET cc_start: 0.6374 (mmm) cc_final: 0.5765 (tmm) REVERT: B 550 ARG cc_start: 0.6421 (tpt170) cc_final: 0.5145 (mmt90) REVERT: C 137 THR cc_start: 0.8764 (t) cc_final: 0.8425 (m) REVERT: C 197 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7614 (ptm-80) REVERT: C 276 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6699 (ptpt) REVERT: C 300 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: C 336 GLU cc_start: 0.8030 (tp30) cc_final: 0.7591 (mm-30) REVERT: C 464 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7405 (mt) REVERT: C 542 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7426 (mp) REVERT: C 546 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6306 (tt0) REVERT: C 547 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7494 (ttt90) REVERT: C 550 ARG cc_start: 0.7592 (mmm160) cc_final: 0.7075 (mtt180) REVERT: C 563 PHE cc_start: 0.8382 (t80) cc_final: 0.8049 (t80) REVERT: C 567 MET cc_start: 0.7439 (mmm) cc_final: 0.6813 (mmm) REVERT: D 62 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5998 (mm-30) REVERT: D 206 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7204 (pt0) REVERT: D 388 ASN cc_start: 0.7388 (m-40) cc_final: 0.7162 (m-40) REVERT: D 407 ASN cc_start: 0.6358 (OUTLIER) cc_final: 0.5923 (m110) REVERT: E 81 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7547 (mpt-90) REVERT: E 109 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: E 209 GLU cc_start: 0.7831 (tt0) cc_final: 0.7566 (mm-30) REVERT: E 336 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: E 345 ARG cc_start: 0.7346 (ttm-80) cc_final: 0.6865 (mtm-85) REVERT: E 410 ARG cc_start: 0.6513 (tpp80) cc_final: 0.6218 (mtm110) REVERT: E 416 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7176 (t70) REVERT: F 3 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6578 (tp) REVERT: F 6 LYS cc_start: 0.7467 (ttpp) cc_final: 0.7054 (ptpt) REVERT: F 53 GLU cc_start: 0.7776 (mp0) cc_final: 0.7382 (mp0) REVERT: F 100 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7485 (pt) REVERT: F 232 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8348 (mp) REVERT: F 305 LYS cc_start: 0.7986 (mttt) cc_final: 0.7424 (mmmt) REVERT: F 388 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7196 (m110) REVERT: G 50 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6643 (mmt90) REVERT: G 181 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: I 104 MET cc_start: 0.4903 (mtm) cc_final: 0.4119 (tmm) REVERT: J 66 LEU cc_start: 0.5383 (mt) cc_final: 0.4876 (tp) REVERT: J 67 LEU cc_start: 0.5850 (mt) cc_final: 0.5399 (tp) REVERT: L 67 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4657 (mm) outliers start: 132 outliers final: 61 residues processed: 476 average time/residue: 0.6903 time to fit residues: 381.6414 Evaluate side-chains 438 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 355 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 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 384 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 570 ILE 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 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 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 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 407 ASN 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 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 21 VAL Chi-restraints excluded: chain F residue 79 VAL 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 316 MET Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 396 VAL 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 50 ARG Chi-restraints excluded: chain G residue 181 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 119 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 353 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS D 407 ASN E 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.154206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120287 restraints weight = 38003.867| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.66 r_work: 0.3232 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30110 Z= 0.124 Angle : 0.530 12.597 40807 Z= 0.265 Chirality : 0.043 0.175 4572 Planarity : 0.005 0.043 5333 Dihedral : 4.965 88.818 4197 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 3.92 % Allowed : 18.13 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3764 helix: 1.70 (0.13), residues: 1584 sheet: -0.58 (0.21), residues: 613 loop : 0.10 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 154 TYR 0.020 0.001 TYR E 13 PHE 0.013 0.001 PHE C 559 TRP 0.012 0.001 TRP J 100 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (30110) covalent geometry : angle 0.52992 / 0.27 (40807) hydrogen bonds : bond 0.03632 / 2.41 ( 1339) hydrogen bonds : angle 4.56653 / 3.25 ( 3822) *********************** 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 490 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 369 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7722 (t70) cc_final: 0.7130 (t70) REVERT: A 98 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7674 (p) REVERT: A 104 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.6278 (mtp85) REVERT: A 124 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7309 (mppt) REVERT: A 130 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7365 (ptt-90) REVERT: A 154 ARG cc_start: 0.7431 (ptm160) cc_final: 0.6874 (ptp90) REVERT: A 449 GLU cc_start: 0.8144 (mp0) cc_final: 0.7941 (mp0) REVERT: A 481 ARG cc_start: 0.7608 (mtp85) cc_final: 0.6974 (ttm110) REVERT: A 517 LYS cc_start: 0.7342 (tptp) cc_final: 0.7102 (tttt) REVERT: A 524 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7372 (tttt) REVERT: B 69 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8037 (mt) REVERT: B 122 MET cc_start: 0.7334 (mtt) cc_final: 0.7021 (mtp) REVERT: B 211 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7775 (tp) REVERT: B 246 ASN cc_start: 0.6866 (t0) cc_final: 0.6527 (t0) REVERT: B 268 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6886 (tp30) REVERT: B 401 ARG cc_start: 0.7307 (mtp85) cc_final: 0.6970 (mtt-85) REVERT: B 509 MET cc_start: 0.6339 (mmm) cc_final: 0.5786 (tmt) REVERT: B 550 ARG cc_start: 0.6362 (tpt170) cc_final: 0.6089 (tpm170) REVERT: C 137 THR cc_start: 0.8763 (t) cc_final: 0.8408 (m) REVERT: C 197 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7642 (ptm-80) REVERT: C 276 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6671 (ptpt) REVERT: C 300 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: C 336 GLU cc_start: 0.8091 (tp30) cc_final: 0.7640 (mm-30) REVERT: C 464 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7413 (mt) REVERT: C 541 GLN cc_start: 0.6623 (mm-40) cc_final: 0.6395 (pt0) REVERT: C 546 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: C 547 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7508 (ttt90) REVERT: C 550 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7089 (mtt180) REVERT: C 563 PHE cc_start: 0.8362 (t80) cc_final: 0.8046 (t80) REVERT: C 567 MET cc_start: 0.7426 (mmm) cc_final: 0.6841 (mmm) REVERT: D 62 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.6024 (mm-30) REVERT: D 206 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7187 (pt0) REVERT: D 388 ASN cc_start: 0.7396 (m-40) cc_final: 0.7188 (m-40) REVERT: E 81 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7577 (mpt-90) REVERT: E 109 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: E 209 GLU cc_start: 0.7861 (tt0) cc_final: 0.7639 (mm-30) REVERT: E 336 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: E 345 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.6835 (mtm-85) REVERT: E 410 ARG cc_start: 0.6703 (tpp80) cc_final: 0.6271 (mtm110) REVERT: E 416 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7217 (t70) REVERT: F 3 LEU cc_start: 0.6925 (tp) cc_final: 0.6574 (tp) REVERT: F 6 LYS cc_start: 0.7462 (ttpp) cc_final: 0.7043 (ptpt) REVERT: F 53 GLU cc_start: 0.7849 (mp0) cc_final: 0.7454 (mp0) REVERT: F 100 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7563 (mm) REVERT: F 232 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8354 (mp) REVERT: F 305 LYS cc_start: 0.8037 (mttt) cc_final: 0.7458 (mmmt) REVERT: F 388 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7179 (m110) REVERT: G 50 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6673 (mmt90) REVERT: G 181 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: G 200 LYS cc_start: 0.7120 (mmmt) cc_final: 0.6522 (mmtt) REVERT: H 103 LYS cc_start: 0.6275 (ttmt) cc_final: 0.5898 (tmmm) REVERT: I 104 MET cc_start: 0.4729 (mtm) cc_final: 0.4121 (tmm) REVERT: J 66 LEU cc_start: 0.5437 (mt) cc_final: 0.4918 (tp) REVERT: J 67 LEU cc_start: 0.5850 (mt) cc_final: 0.5395 (tp) REVERT: K 104 MET cc_start: 0.5317 (tpp) cc_final: 0.4328 (mpp) REVERT: L 67 LEU cc_start: 0.4956 (OUTLIER) cc_final: 0.4608 (mm) outliers start: 121 outliers final: 65 residues processed: 458 average time/residue: 0.7421 time to fit residues: 392.5800 Evaluate side-chains 435 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 352 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN 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 496 GLN 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 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 292 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 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 464 LEU 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 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 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 405 THR 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 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 470 ILE Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 79 VAL 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 396 VAL 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 33 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 51 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 276 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 465 GLN C 109 HIS D 407 ASN E 23 ASN E 427 GLN F 23 ASN G 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.155071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120004 restraints weight = 37748.431| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.67 r_work: 0.3144 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30110 Z= 0.233 Angle : 0.642 12.359 40807 Z= 0.325 Chirality : 0.047 0.185 4572 Planarity : 0.006 0.053 5333 Dihedral : 5.439 89.896 4197 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 4.41 % Allowed : 18.10 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3764 helix: 1.30 (0.13), residues: 1581 sheet: -0.67 (0.20), residues: 614 loop : -0.08 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 154 TYR 0.025 0.002 TYR A 439 PHE 0.021 0.002 PHE C 559 TRP 0.022 0.002 TRP J 100 HIS 0.006 0.001 HIS F 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.23 (30110) covalent geometry : angle 0.64214 / 0.32 (40807) hydrogen bonds : bond 0.04638 / 3.07 ( 1339) hydrogen bonds : angle 4.84087 / 3.46 ( 3822) *********************** 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 495 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 359 time to evaluate : 1.113 Fit side-chains REVERT: A 53 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: A 104 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.6430 (mtp85) REVERT: A 130 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7349 (ptt-90) REVERT: A 154 ARG cc_start: 0.7420 (ptm160) cc_final: 0.6846 (ptp90) REVERT: A 456 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: A 481 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7039 (ttm110) REVERT: A 517 LYS cc_start: 0.7351 (tptp) cc_final: 0.7122 (tttt) REVERT: B 69 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7898 (mt) REVERT: B 122 MET cc_start: 0.7534 (mtt) cc_final: 0.7222 (mtp) REVERT: B 161 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7615 (mmmm) REVERT: B 211 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7876 (tp) REVERT: B 246 ASN cc_start: 0.6818 (t0) cc_final: 0.6464 (t0) REVERT: B 268 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6828 (tp30) REVERT: B 401 ARG cc_start: 0.7381 (mtp85) cc_final: 0.6946 (mtt-85) REVERT: B 509 MET cc_start: 0.6637 (mmm) cc_final: 0.5878 (tmt) REVERT: B 548 ILE cc_start: 0.6511 (mm) cc_final: 0.6252 (mm) REVERT: C 137 THR cc_start: 0.8775 (t) cc_final: 0.8409 (m) REVERT: C 197 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7679 (ptm-80) REVERT: C 276 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6697 (ptpt) REVERT: C 300 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: C 336 GLU cc_start: 0.8139 (tp30) cc_final: 0.7725 (mm-30) REVERT: C 546 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: C 547 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7507 (ttt90) REVERT: C 563 PHE cc_start: 0.8502 (t80) cc_final: 0.8268 (t80) REVERT: C 567 MET cc_start: 0.7499 (mmm) cc_final: 0.6877 (mmm) REVERT: D 49 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: D 62 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6115 (mm-30) REVERT: D 206 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7203 (pt0) REVERT: E 81 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7615 (mpt-90) REVERT: E 109 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6862 (tp30) REVERT: E 209 GLU cc_start: 0.7993 (tt0) cc_final: 0.7700 (mm-30) REVERT: E 336 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: E 345 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6799 (mtm-85) REVERT: E 410 ARG cc_start: 0.6681 (tpp80) cc_final: 0.6371 (mtm110) REVERT: E 416 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7297 (t70) REVERT: E 470 ILE cc_start: 0.2098 (OUTLIER) cc_final: 0.1810 (pt) REVERT: F 3 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6534 (tp) REVERT: F 6 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7081 (ptpt) REVERT: F 53 GLU cc_start: 0.7826 (mp0) cc_final: 0.7458 (mp0) REVERT: F 280 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7402 (mtm180) REVERT: F 305 LYS cc_start: 0.8130 (mttt) cc_final: 0.7582 (mmmt) REVERT: F 388 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7340 (m110) REVERT: G 13 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8165 (tm-30) REVERT: G 200 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6515 (mmtt) REVERT: H 63 MET cc_start: 0.3492 (pmm) cc_final: 0.2303 (mtm) REVERT: I 104 MET cc_start: 0.4717 (mtm) cc_final: 0.4182 (tmm) REVERT: J 66 LEU cc_start: 0.5498 (mt) cc_final: 0.4942 (tp) REVERT: J 67 LEU cc_start: 0.5862 (mt) cc_final: 0.5371 (tp) REVERT: J 119 LYS cc_start: 0.6423 (tttt) cc_final: 0.5401 (tmtt) REVERT: K 104 MET cc_start: 0.5211 (OUTLIER) cc_final: 0.4185 (mpp) REVERT: L 67 LEU cc_start: 0.5164 (OUTLIER) cc_final: 0.4739 (mm) outliers start: 136 outliers final: 67 residues processed: 455 average time/residue: 0.7506 time to fit residues: 394.6208 Evaluate side-chains 432 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 345 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 119 TRP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL 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 B residue 69 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 268 GLU 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 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 464 LEU 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 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 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 405 THR 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 173 VAL Chi-restraints excluded: chain E residue 177 LEU 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 21 VAL 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 149 LYS 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 396 VAL 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 J residue 128 LEU 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 260 optimal weight: 0.8980 chunk 359 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 348 optimal weight: 0.1980 chunk 237 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 350 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN C 109 HIS D 407 ASN E 23 ASN F 23 ASN F 142 ASN G 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.156347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122956 restraints weight = 37625.908| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.50 r_work: 0.3218 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30110 Z= 0.136 Angle : 0.552 13.870 40807 Z= 0.277 Chirality : 0.044 0.155 4572 Planarity : 0.005 0.045 5333 Dihedral : 5.108 85.346 4197 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.63 % Allowed : 19.01 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3764 helix: 1.49 (0.13), residues: 1588 sheet: -0.68 (0.21), residues: 610 loop : -0.01 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 154 TYR 0.020 0.001 TYR A 439 PHE 0.015 0.001 PHE E 130 TRP 0.016 0.001 TRP J 100 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (30110) covalent geometry : angle 0.55219 / 0.28 (40807) hydrogen bonds : bond 0.03833 / 2.55 ( 1339) hydrogen bonds : angle 4.64336 / 3.31 ( 3822) *********************** 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 475 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 363 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: A 54 ASP cc_start: 0.7791 (t70) cc_final: 0.7180 (t70) REVERT: A 98 THR cc_start: 0.8063 (m) cc_final: 0.7805 (p) REVERT: A 104 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.6316 (mtp85) REVERT: A 130 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7343 (ptt-90) REVERT: A 154 ARG cc_start: 0.7365 (ptm160) cc_final: 0.6836 (ptp90) REVERT: A 158 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7457 (tttt) REVERT: A 190 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8070 (mtt-85) REVERT: A 261 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8361 (mm-30) REVERT: A 323 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8027 (mpp) REVERT: A 449 GLU cc_start: 0.8174 (mp0) cc_final: 0.7927 (mp0) REVERT: A 481 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7025 (ttm110) REVERT: A 532 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.5824 (ttm-80) REVERT: B 69 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7890 (mt) REVERT: B 122 MET cc_start: 0.7401 (mtt) cc_final: 0.7104 (mtp) REVERT: B 211 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7759 (tp) REVERT: B 246 ASN cc_start: 0.6847 (t0) cc_final: 0.6540 (t0) REVERT: B 268 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6867 (tp30) REVERT: B 401 ARG cc_start: 0.7350 (mtp85) cc_final: 0.6962 (mtt-85) REVERT: B 550 ARG cc_start: 0.6772 (tpm170) cc_final: 0.4918 (tpp80) REVERT: C 137 THR cc_start: 0.8791 (t) cc_final: 0.8402 (m) REVERT: C 197 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7598 (ptm-80) REVERT: C 276 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6670 (ptpt) REVERT: C 300 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: C 336 GLU cc_start: 0.8065 (tp30) cc_final: 0.7636 (mm-30) REVERT: C 464 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7408 (mt) REVERT: C 546 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: C 547 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7502 (ttt90) REVERT: C 563 PHE cc_start: 0.8401 (t80) cc_final: 0.8145 (t80) REVERT: C 567 MET cc_start: 0.7418 (mmm) cc_final: 0.6787 (mmm) REVERT: D 49 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: D 62 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5963 (mm-30) REVERT: D 109 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: D 206 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7277 (pt0) REVERT: E 81 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7541 (mpt-90) REVERT: E 209 GLU cc_start: 0.7928 (tt0) cc_final: 0.7683 (mm-30) REVERT: E 345 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6841 (mtm-85) REVERT: E 410 ARG cc_start: 0.6743 (tpp80) cc_final: 0.6388 (mtm110) REVERT: F 3 LEU cc_start: 0.6766 (tp) cc_final: 0.6451 (tp) REVERT: F 6 LYS cc_start: 0.7428 (ttpp) cc_final: 0.7019 (ptpt) REVERT: F 53 GLU cc_start: 0.7759 (mp0) cc_final: 0.7398 (mp0) REVERT: F 305 LYS cc_start: 0.8095 (mttt) cc_final: 0.7591 (mmmt) REVERT: G 13 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8028 (tm-30) REVERT: G 200 LYS cc_start: 0.7091 (mmmt) cc_final: 0.6567 (mmtt) REVERT: H 68 LEU cc_start: 0.4361 (tp) cc_final: 0.3478 (pt) REVERT: H 95 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5744 (tmt170) REVERT: H 103 LYS cc_start: 0.6269 (ttmt) cc_final: 0.5844 (tmmm) REVERT: I 104 MET cc_start: 0.4675 (mtm) cc_final: 0.4238 (tmm) REVERT: J 66 LEU cc_start: 0.5472 (mt) cc_final: 0.4955 (tp) REVERT: J 67 LEU cc_start: 0.5846 (mt) cc_final: 0.5312 (tp) REVERT: J 85 ARG cc_start: 0.4673 (ptp-110) cc_final: 0.4188 (mpt-90) REVERT: J 158 GLU cc_start: 0.6407 (tp30) cc_final: 0.6123 (tp30) REVERT: K 104 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4226 (mpp) REVERT: L 67 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4524 (mm) outliers start: 112 outliers final: 61 residues processed: 445 average time/residue: 0.7756 time to fit residues: 398.4321 Evaluate side-chains 425 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 346 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 393 GLU 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 69 LEU Chi-restraints excluded: chain B residue 92 GLU 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 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 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 300 GLU 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 530 ILE 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 59 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 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 177 LEU 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 358 LEU Chi-restraints excluded: chain F residue 21 VAL 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 250 ASP 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 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 95 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 175 optimal weight: 3.9990 chunk 364 optimal weight: 0.2980 chunk 153 optimal weight: 0.0060 chunk 123 optimal weight: 0.0070 chunk 305 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 341 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 109 HIS D 407 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 = 0.3780 r_free = 0.3780 target = 0.157873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122987 restraints weight = 37636.624| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.78 r_work: 0.3218 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 30110 Z= 0.105 Angle : 0.517 14.572 40807 Z= 0.258 Chirality : 0.042 0.188 4572 Planarity : 0.004 0.052 5333 Dihedral : 4.761 80.149 4197 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.50 % Allowed : 20.43 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.14), residues: 3764 helix: 1.70 (0.13), residues: 1593 sheet: -0.61 (0.21), residues: 595 loop : 0.16 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 154 TYR 0.014 0.001 TYR A 439 PHE 0.011 0.001 PHE C 574 TRP 0.014 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (30110) covalent geometry : angle 0.51698 / 0.26 (40807) hydrogen bonds : bond 0.03331 / 2.21 ( 1339) hydrogen bonds : angle 4.45789 / 3.16 ( 3822) *********************** 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 461 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 384 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8182 (mmp80) cc_final: 0.7904 (mmp80) REVERT: A 98 THR cc_start: 0.7985 (m) cc_final: 0.7715 (p) REVERT: A 130 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7338 (ptt-90) REVERT: A 154 ARG cc_start: 0.7385 (ptm160) cc_final: 0.6831 (ptp90) REVERT: A 261 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 449 GLU cc_start: 0.8168 (mp0) cc_final: 0.7942 (mp0) REVERT: A 481 ARG cc_start: 0.7546 (mtp85) cc_final: 0.6881 (ttm110) REVERT: A 550 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.5901 (mtt180) REVERT: B 122 MET cc_start: 0.7345 (mtt) cc_final: 0.7056 (mtp) REVERT: B 133 MET cc_start: 0.8081 (mtm) cc_final: 0.7800 (mtp) REVERT: B 211 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7769 (tp) REVERT: B 246 ASN cc_start: 0.6808 (t0) cc_final: 0.6577 (t0) REVERT: B 268 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6867 (tp30) REVERT: B 401 ARG cc_start: 0.7338 (mtp85) cc_final: 0.6980 (mtt-85) REVERT: B 435 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7521 (mp) REVERT: C 137 THR cc_start: 0.8765 (t) cc_final: 0.8359 (m) REVERT: C 197 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7665 (ptm-80) REVERT: C 276 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6560 (ptpt) REVERT: C 336 GLU cc_start: 0.8149 (tp30) cc_final: 0.7685 (mm-30) REVERT: C 546 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6313 (tt0) REVERT: C 547 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7452 (ttt90) REVERT: C 550 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7055 (mtt180) REVERT: C 563 PHE cc_start: 0.8259 (t80) cc_final: 0.8033 (t80) REVERT: C 567 MET cc_start: 0.7348 (mmm) cc_final: 0.6794 (mmm) REVERT: D 62 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5942 (mm-30) REVERT: D 206 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7095 (pp30) REVERT: E 25 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7820 (mtpt) REVERT: E 209 GLU cc_start: 0.7893 (tt0) cc_final: 0.7692 (mm-30) REVERT: E 345 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.6726 (mtm-85) REVERT: E 410 ARG cc_start: 0.6799 (tpp80) cc_final: 0.6355 (mtm110) REVERT: E 416 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7246 (t70) REVERT: F 3 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6436 (tp) REVERT: F 6 LYS cc_start: 0.7427 (ttpp) cc_final: 0.7020 (ptpt) REVERT: F 53 GLU cc_start: 0.7838 (mp0) cc_final: 0.7431 (mp0) REVERT: F 305 LYS cc_start: 0.8122 (mttt) cc_final: 0.7526 (mmmt) REVERT: F 466 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.7012 (ptpt) REVERT: G 51 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.5483 (pttp) REVERT: G 200 LYS cc_start: 0.6966 (mmmt) cc_final: 0.6523 (mmtt) REVERT: H 63 MET cc_start: 0.3563 (pmm) cc_final: 0.2307 (mtm) REVERT: H 95 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5651 (tmt170) REVERT: H 98 ILE cc_start: 0.5567 (pt) cc_final: 0.5322 (pp) REVERT: H 103 LYS cc_start: 0.6221 (ttmt) cc_final: 0.5832 (tmmm) REVERT: I 104 MET cc_start: 0.4762 (mtm) cc_final: 0.4253 (tmm) REVERT: J 66 LEU cc_start: 0.5463 (mt) cc_final: 0.4913 (tp) REVERT: J 67 LEU cc_start: 0.5697 (mt) cc_final: 0.5232 (tp) REVERT: J 85 ARG cc_start: 0.4635 (ptp-110) cc_final: 0.4158 (mpt-90) REVERT: J 128 LEU cc_start: 0.4496 (OUTLIER) cc_final: 0.3957 (pp) REVERT: K 104 MET cc_start: 0.5127 (tpp) cc_final: 0.4166 (mpp) REVERT: L 67 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.4454 (mm) outliers start: 77 outliers final: 43 residues processed: 435 average time/residue: 0.7392 time to fit residues: 372.0181 Evaluate side-chains 413 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 357 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 92 GLU 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 B residue 384 VAL Chi-restraints excluded: chain B residue 435 LEU 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 276 LYS 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 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 79 VAL 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 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 21 VAL 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 149 LYS Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 466 LYS 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 J residue 128 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 270 optimal weight: 1.9990 chunk 240 optimal weight: 0.0060 chunk 150 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 252 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS D 407 ASN E 23 ASN F 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121436 restraints weight = 37736.428| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.75 r_work: 0.3212 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30110 Z= 0.119 Angle : 0.534 15.429 40807 Z= 0.266 Chirality : 0.043 0.212 4572 Planarity : 0.005 0.053 5333 Dihedral : 4.789 79.003 4197 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.27 % Allowed : 21.05 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3764 helix: 1.74 (0.13), residues: 1593 sheet: -0.60 (0.21), residues: 605 loop : 0.19 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 154 TYR 0.025 0.001 TYR E 13 PHE 0.013 0.001 PHE C 559 TRP 0.011 0.001 TRP J 100 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (30110) covalent geometry : angle 0.53441 / 0.27 (40807) hydrogen bonds : bond 0.03459 / 2.29 ( 1339) hydrogen bonds : angle 4.47242 / 3.18 ( 3822) ********************** 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 420 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 350 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.7994 (m) cc_final: 0.7717 (p) REVERT: A 130 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7337 (ptt-90) REVERT: A 154 ARG cc_start: 0.7400 (ptm160) cc_final: 0.6834 (ptp90) REVERT: A 158 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7309 (tttt) REVERT: A 202 ASN cc_start: 0.8150 (p0) cc_final: 0.7862 (p0) REVERT: A 261 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8348 (mm-30) REVERT: A 449 GLU cc_start: 0.8188 (mp0) cc_final: 0.7974 (mp0) REVERT: A 481 ARG cc_start: 0.7573 (mtp85) cc_final: 0.6774 (ttp-110) REVERT: B 122 MET cc_start: 0.7371 (mtt) cc_final: 0.7064 (mtp) REVERT: B 211 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7832 (tp) REVERT: B 246 ASN cc_start: 0.6786 (t0) cc_final: 0.6570 (t0) REVERT: B 268 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6853 (tp30) REVERT: B 401 ARG cc_start: 0.7351 (mtp85) cc_final: 0.7011 (mtt-85) REVERT: B 548 ILE cc_start: 0.5744 (mm) cc_final: 0.4383 (tt) REVERT: B 550 ARG cc_start: 0.6534 (tpm170) cc_final: 0.4918 (mtp85) REVERT: C 137 THR cc_start: 0.8801 (t) cc_final: 0.8433 (m) REVERT: C 197 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7642 (ptm-80) REVERT: C 276 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6568 (ptpt) REVERT: C 336 GLU cc_start: 0.8149 (tp30) cc_final: 0.7691 (mm-30) REVERT: C 546 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6305 (tm-30) REVERT: C 547 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7362 (ttt90) REVERT: C 563 PHE cc_start: 0.8256 (t80) cc_final: 0.7995 (t80) REVERT: C 567 MET cc_start: 0.7392 (mmm) cc_final: 0.6778 (mmm) REVERT: D 49 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: D 62 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5962 (mm-30) REVERT: D 206 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7173 (pt0) REVERT: D 407 ASN cc_start: 0.6360 (OUTLIER) cc_final: 0.5896 (m110) REVERT: E 345 ARG cc_start: 0.7359 (ttm-80) cc_final: 0.6751 (mtm-85) REVERT: E 410 ARG cc_start: 0.6890 (tpp80) cc_final: 0.6431 (mtm110) REVERT: E 416 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7285 (t70) REVERT: F 3 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6439 (tp) REVERT: F 6 LYS cc_start: 0.7452 (ttpp) cc_final: 0.7035 (ptpt) REVERT: F 53 GLU cc_start: 0.7836 (mp0) cc_final: 0.7429 (mp0) REVERT: F 305 LYS cc_start: 0.8145 (mttt) cc_final: 0.7543 (mmmt) REVERT: F 466 LYS cc_start: 0.7319 (pttt) cc_final: 0.7104 (ptpt) REVERT: G 51 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5453 (pttp) REVERT: G 200 LYS cc_start: 0.6862 (mmmt) cc_final: 0.6453 (mmtt) REVERT: H 68 LEU cc_start: 0.4114 (tp) cc_final: 0.3220 (pt) REVERT: H 95 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.5679 (tmt170) REVERT: H 98 ILE cc_start: 0.5595 (pt) cc_final: 0.5347 (pp) REVERT: H 103 LYS cc_start: 0.6211 (ttmt) cc_final: 0.5830 (tmmm) REVERT: I 104 MET cc_start: 0.4744 (mtm) cc_final: 0.4222 (tmm) REVERT: J 66 LEU cc_start: 0.5438 (mt) cc_final: 0.4894 (tp) REVERT: J 67 LEU cc_start: 0.5755 (mt) cc_final: 0.5259 (tp) REVERT: J 82 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6007 (mm-30) REVERT: J 128 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.3924 (pp) REVERT: K 104 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.4233 (mpp) REVERT: L 67 LEU cc_start: 0.4893 (OUTLIER) cc_final: 0.4460 (mm) outliers start: 70 outliers final: 43 residues processed: 396 average time/residue: 0.7566 time to fit residues: 346.3588 Evaluate side-chains 401 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 92 GLU 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 B residue 384 VAL 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 276 LYS 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 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 407 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 21 VAL 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 149 LYS 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 H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain J residue 122 VAL 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 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 267 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 25 optimal weight: 0.0470 chunk 128 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 356 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 358 optimal weight: 0.7980 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124263 restraints weight = 37651.623| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.71 r_work: 0.3230 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.169 30110 Z= 0.172 Angle : 0.656 59.200 40807 Z= 0.365 Chirality : 0.045 0.817 4572 Planarity : 0.005 0.061 5333 Dihedral : 4.815 78.998 4197 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 21.21 % Favored : 76.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1593 sheet: -0.60 (0.21), residues: 605 loop : 0.20 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 154 TYR 0.015 0.001 TYR A 439 PHE 0.013 0.001 PHE C 559 TRP 0.013 0.001 TRP L 175 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (30110) covalent geometry : angle 0.65576 / 0.37 (40807) hydrogen bonds : bond 0.03484 / 2.31 ( 1339) hydrogen bonds : angle 4.47459 / 3.18 ( 3822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11843.25 seconds wall clock time: 201 minutes 55.23 seconds (12115.23 seconds total)