Starting phenix.real_space_refine on Sun Jul 5 17:37:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vap_31857/07_2026/7vap_31857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vap_31857/07_2026/7vap_31857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vap_31857/07_2026/7vap_31857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vap_31857/07_2026/7vap_31857.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vap_31857/07_2026/7vap_31857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vap_31857/07_2026/7vap_31857.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vap_31857/07_2026/7vap_31857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vap_31857/07_2026/7vap_31857.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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.59, per 1000 atoms: 0.22 Number of scatterers: 29558 At special positions: 0 Unit cell: (136.4, 147.84, 176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 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: 145 helices and 24 sheets defined 47.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.021A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.106A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.564A pdb=" N ASP A 390 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.602A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.550A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.790A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.620A 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 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.982A 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 576 removed outlier: 3.531A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.566A pdb=" N PHE B 269 " --> pdb=" O VAL B 265 " (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: 5.015A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.692A 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 removed outlier: 3.917A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 removed outlier: 3.553A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.928A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.682A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.582A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.827A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.201A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.132A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.542A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.552A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.551A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.015A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.296A 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 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.552A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.695A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.608A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.757A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.576A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.528A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.965A 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 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.750A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.508A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 removed outlier: 3.645A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.774A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.468A 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: 4.200A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 175 through 179 removed outlier: 3.627A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.043A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.970A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.801A 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: 3.909A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.568A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.029A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.505A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.823A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.656A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) 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: 3.945A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 361 through 366' Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.516A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.950A 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: 3.564A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 470 removed outlier: 3.503A pdb=" N GLU F 469 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.794A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.636A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 209 removed outlier: 3.572A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.604A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.921A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 5.889A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 4.118A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.790A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.560A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.589A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 3.625A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 93 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 166 through 187 removed outlier: 5.082A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.587A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.664A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.751A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.826A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.680A 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 50 removed outlier: 5.461A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.820A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.784A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.589A 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: 6.587A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.758A 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: 3.625A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.808A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.795A 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 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.604A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.549A 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: 3.560A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.858A 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: 3.718A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 91 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 93 current: chain 'D' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 223 current: chain 'D' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 307 through 315 current: chain 'D' and resid 358 through 359 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.716A 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: 6.737A pdb=" N ARG E 91 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU E 221 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.504A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.510A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 94 current: chain 'F' and resid 217 through 221 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 221 current: chain 'F' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 307 through 315 current: chain 'F' and resid 358 through 359 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.794A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 91 through 96 Processing sheet with id=AC6, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.778A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1274 hydrogen bonds defined for protein. 3651 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: 5.94 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9959 1.34 - 1.46: 4212 1.46 - 1.57: 15740 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.449 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.474 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.473 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.430 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.496 0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 40432 2.23 - 4.46: 326 4.46 - 6.69: 48 6.69 - 8.92: 6 8.92 - 11.15: 1 Bond angle restraints: 40813 Sorted by residual: angle pdb=" C THR E 371 " pdb=" CA THR E 371 " pdb=" CB THR E 371 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 angle pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 108.20 97.05 11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA THR E 371 " pdb=" C THR E 371 " pdb=" N ARG E 372 " ideal model delta sigma weight residual 119.98 117.37 2.61 8.50e-01 1.38e+00 9.40e+00 angle pdb=" CA ILE A 402 " pdb=" C ILE A 402 " pdb=" N VAL A 403 " ideal model delta sigma weight residual 116.60 120.71 -4.11 1.45e+00 4.76e-01 8.05e+00 angle pdb=" C PHE C 419 " pdb=" N PRO C 420 " pdb=" CA PRO C 420 " ideal model delta sigma weight residual 127.00 133.66 -6.66 2.40e+00 1.74e-01 7.70e+00 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 17835 30.14 - 60.27: 421 60.27 - 90.41: 64 90.41 - 120.55: 0 120.55 - 150.69: 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 300.00 149.32 150.69 1 2.00e+01 2.50e-03 4.49e+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 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -134.15 74.14 1 2.00e+01 2.50e-03 1.74e+01 ... (remaining 18318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3437 0.045 - 0.091: 837 0.091 - 0.136: 287 0.136 - 0.181: 9 0.181 - 0.227: 2 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE C 83 " pdb=" CA ILE C 83 " pdb=" CG1 ILE C 83 " pdb=" CG2 ILE C 83 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 394 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO D 324 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 393 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 394 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 394 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 394 " 0.023 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.30: 14 2.30 - 2.95: 12825 2.95 - 3.60: 42092 3.60 - 4.25: 67651 4.25 - 4.90: 116962 Nonbonded interactions: 239544 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.645 2.170 nonbonded pdb=" O2B ADP A 601 " pdb="MG MG A 602 " model vdw 1.882 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.953 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 2.003 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.078 2.170 ... (remaining 239539 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.860 Find NCS groups from input model: 0.690 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: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 30114 Z= 0.181 Angle : 0.538 11.153 40813 Z= 0.282 Chirality : 0.043 0.227 4572 Planarity : 0.004 0.048 5333 Dihedral : 13.360 150.687 11403 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.14), residues: 3764 helix: 2.09 (0.14), residues: 1537 sheet: 0.27 (0.23), residues: 570 loop : 0.20 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 364 TYR 0.011 0.001 TYR D 463 PHE 0.016 0.001 PHE A 230 TRP 0.008 0.001 TRP C 119 HIS 0.006 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (30114) covalent geometry : angle 0.53781 / 0.28 (40813) hydrogen bonds : bond 0.14406 / 9.73 ( 1274) hydrogen bonds : angle 5.81521 / 4.04 ( 3651) *********************** 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 597 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7281 (mt0) cc_final: 0.6916 (mt0) REVERT: A 38 GLU cc_start: 0.7692 (tt0) cc_final: 0.7111 (tt0) REVERT: A 97 LYS cc_start: 0.6905 (mttt) cc_final: 0.6603 (mttt) REVERT: A 115 LYS cc_start: 0.8168 (tttp) cc_final: 0.7826 (tttt) REVERT: A 209 MET cc_start: 0.7207 (mtp) cc_final: 0.6840 (mtt) REVERT: A 240 SER cc_start: 0.8399 (m) cc_final: 0.8098 (p) REVERT: A 273 THR cc_start: 0.8227 (m) cc_final: 0.7982 (t) REVERT: A 343 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7056 (mt-10) REVERT: A 344 MET cc_start: 0.7568 (tpt) cc_final: 0.6584 (tmm) REVERT: A 441 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6937 (mm-30) REVERT: A 456 GLU cc_start: 0.5773 (mt-10) cc_final: 0.5470 (mt-10) REVERT: A 466 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5770 (tt0) REVERT: A 491 ARG cc_start: 0.6800 (mmt180) cc_final: 0.5666 (mtm-85) REVERT: A 538 GLU cc_start: 0.5273 (tm-30) cc_final: 0.5071 (tm-30) REVERT: A 555 SER cc_start: 0.7320 (t) cc_final: 0.6953 (p) REVERT: B 96 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6665 (mt-10) REVERT: B 124 LYS cc_start: 0.7096 (mtmm) cc_final: 0.6280 (mptt) REVERT: B 152 ASP cc_start: 0.6506 (m-30) cc_final: 0.6238 (p0) REVERT: B 156 ARG cc_start: 0.6803 (ttm170) cc_final: 0.6358 (ttm110) REVERT: B 159 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6303 (mm-30) REVERT: B 165 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 179 THR cc_start: 0.7030 (m) cc_final: 0.6586 (t) REVERT: B 220 MET cc_start: 0.7598 (ttp) cc_final: 0.7326 (ttm) REVERT: B 241 LEU cc_start: 0.7435 (mt) cc_final: 0.7126 (tt) REVERT: B 264 ASP cc_start: 0.6822 (m-30) cc_final: 0.6543 (m-30) REVERT: B 268 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 276 LYS cc_start: 0.6474 (mttt) cc_final: 0.5664 (ttpp) REVERT: B 294 MET cc_start: 0.7623 (mtp) cc_final: 0.7378 (mmm) REVERT: B 323 MET cc_start: 0.8237 (mtt) cc_final: 0.8017 (mtm) REVERT: B 374 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 393 GLU cc_start: 0.6535 (tt0) cc_final: 0.6217 (tt0) REVERT: B 397 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6844 (mt0) REVERT: B 408 ARG cc_start: 0.7213 (ttm170) cc_final: 0.6857 (tpp80) REVERT: B 460 ARG cc_start: 0.6023 (mtp180) cc_final: 0.5742 (mmm160) REVERT: B 488 ARG cc_start: 0.5607 (ttp-110) cc_final: 0.5400 (tmm160) REVERT: B 489 ILE cc_start: 0.6381 (mt) cc_final: 0.6081 (mt) REVERT: B 541 GLN cc_start: 0.5415 (mp10) cc_final: 0.4656 (mt0) REVERT: B 547 ARG cc_start: 0.5101 (mmm-85) cc_final: 0.4548 (mmt180) REVERT: B 558 GLU cc_start: 0.5619 (tt0) cc_final: 0.5096 (tp30) REVERT: C 107 VAL cc_start: 0.8674 (m) cc_final: 0.8355 (t) REVERT: C 146 LYS cc_start: 0.7859 (mttp) cc_final: 0.7617 (mtpp) REVERT: C 154 ARG cc_start: 0.7086 (mtp-110) cc_final: 0.6850 (mtm-85) REVERT: C 159 GLU cc_start: 0.7352 (pt0) cc_final: 0.6722 (pp20) REVERT: C 165 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6815 (mt-10) REVERT: C 342 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7207 (mm-30) REVERT: C 412 SER cc_start: 0.7893 (m) cc_final: 0.7597 (p) REVERT: C 424 TRP cc_start: 0.7406 (p90) cc_final: 0.6980 (p-90) REVERT: C 480 GLU cc_start: 0.6601 (mp0) cc_final: 0.6220 (mm-30) REVERT: C 481 ARG cc_start: 0.6234 (mmm-85) cc_final: 0.5796 (mmm-85) REVERT: C 492 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6933 (mt-10) REVERT: C 530 ILE cc_start: 0.6711 (mt) cc_final: 0.6363 (mt) REVERT: C 538 GLU cc_start: 0.6385 (mt-10) cc_final: 0.5399 (mm-30) REVERT: C 565 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5795 (mt-10) REVERT: C 571 GLN cc_start: 0.6583 (mp10) cc_final: 0.6205 (mt0) REVERT: D 6 LYS cc_start: 0.6866 (tttp) cc_final: 0.6620 (tptp) REVERT: D 34 ASP cc_start: 0.7200 (m-30) cc_final: 0.6813 (p0) REVERT: D 49 GLU cc_start: 0.7029 (tt0) cc_final: 0.6726 (tt0) REVERT: D 77 GLU cc_start: 0.6652 (tt0) cc_final: 0.6415 (mt-10) REVERT: D 98 LYS cc_start: 0.7694 (mmmm) cc_final: 0.7281 (mmpt) REVERT: D 175 PRO cc_start: 0.7294 (Cg_endo) cc_final: 0.6952 (Cg_exo) REVERT: D 223 LYS cc_start: 0.7446 (mtpp) cc_final: 0.6814 (mtpt) REVERT: D 260 MET cc_start: 0.7931 (mmm) cc_final: 0.7688 (mmm) REVERT: D 264 CYS cc_start: 0.7552 (m) cc_final: 0.7128 (m) REVERT: D 305 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7304 (mtmm) REVERT: D 321 ARG cc_start: 0.7436 (mtp180) cc_final: 0.7210 (tpp80) REVERT: D 362 MET cc_start: 0.8446 (ttt) cc_final: 0.8054 (ttt) REVERT: D 421 PHE cc_start: 0.7374 (m-80) cc_final: 0.6883 (m-10) REVERT: D 452 LYS cc_start: 0.7310 (mmtp) cc_final: 0.7018 (mmtp) REVERT: E 7 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6729 (OUTLIER) REVERT: E 26 ASP cc_start: 0.7523 (p0) cc_final: 0.7287 (p0) REVERT: E 49 GLU cc_start: 0.7589 (tt0) cc_final: 0.7288 (tt0) REVERT: E 81 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7045 (mtt-85) REVERT: E 302 GLU cc_start: 0.7062 (tt0) cc_final: 0.6830 (tp30) REVERT: E 305 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7377 (mmtp) REVERT: E 353 ASP cc_start: 0.7883 (t0) cc_final: 0.7667 (t70) REVERT: E 376 LYS cc_start: 0.6996 (tttm) cc_final: 0.6493 (ttpt) REVERT: E 420 ARG cc_start: 0.6852 (mtm110) cc_final: 0.6418 (mtm-85) REVERT: E 427 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7899 (mm110) REVERT: E 428 GLN cc_start: 0.6899 (tt0) cc_final: 0.6663 (mt0) REVERT: E 465 GLN cc_start: 0.6090 (tt0) cc_final: 0.5623 (mm110) REVERT: F 7 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7197 (mt-10) REVERT: F 9 THR cc_start: 0.7851 (m) cc_final: 0.7456 (p) REVERT: F 53 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6323 (mp0) REVERT: F 81 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7549 (mtt-85) REVERT: F 110 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7691 (mtmt) REVERT: F 129 GLN cc_start: 0.7696 (mm110) cc_final: 0.7481 (tp-100) REVERT: F 248 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7275 (mt-10) REVERT: F 305 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7201 (mttm) REVERT: F 409 ARG cc_start: 0.7047 (ttm-80) cc_final: 0.6712 (ttm-80) REVERT: F 410 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6552 (mtt90) REVERT: F 437 GLN cc_start: 0.7004 (tt0) cc_final: 0.5981 (mm-40) REVERT: F 445 MET cc_start: 0.8208 (mtt) cc_final: 0.7775 (mtp) REVERT: F 452 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6735 (mtmt) REVERT: F 457 ASP cc_start: 0.5956 (m-30) cc_final: 0.5657 (t0) REVERT: G 17 GLN cc_start: 0.6420 (mm-40) cc_final: 0.6108 (tp40) REVERT: G 155 LYS cc_start: 0.5485 (mttt) cc_final: 0.4815 (tppt) REVERT: G 160 ARG cc_start: 0.5448 (mmm-85) cc_final: 0.5204 (tpp80) REVERT: G 197 ILE cc_start: 0.6132 (pt) cc_final: 0.5430 (mm) REVERT: G 200 LYS cc_start: 0.5440 (mttm) cc_final: 0.5226 (mtpp) REVERT: J 158 GLU cc_start: 0.4026 (tp30) cc_final: 0.3796 (mt-10) REVERT: J 170 ARG cc_start: 0.3064 (mtp85) cc_final: 0.2812 (mtp85) REVERT: L 158 GLU cc_start: 0.4564 (mm-30) cc_final: 0.3968 (pt0) outliers start: 0 outliers final: 3 residues processed: 597 average time/residue: 0.8786 time to fit residues: 592.1225 Evaluate side-chains 361 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain B residue 515 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 GLN A 469 GLN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 283 HIS D 170 GLN D 252 HIS D 310 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN E 222 ASN E 407 ASN F 388 ASN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108223 restraints weight = 38348.377| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.91 r_work: 0.2978 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 30114 Z= 0.244 Angle : 0.698 9.037 40813 Z= 0.360 Chirality : 0.050 0.189 4572 Planarity : 0.006 0.052 5333 Dihedral : 5.924 153.740 4201 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.92 % Allowed : 8.50 % Favored : 88.58 % 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: 0.59 (0.14), residues: 3764 helix: 1.28 (0.13), residues: 1563 sheet: 0.02 (0.22), residues: 557 loop : -0.25 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 460 TYR 0.020 0.002 TYR A 25 PHE 0.028 0.003 PHE C 230 TRP 0.026 0.002 TRP C 119 HIS 0.020 0.002 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.24 (30114) covalent geometry : angle 0.69787 / 0.36 (40813) hydrogen bonds : bond 0.06033 / 4.04 ( 1274) hydrogen bonds : angle 4.95161 / 3.48 ( 3651) *********************** 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 450 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 360 time to evaluate : 1.174 Fit side-chains REVERT: A 3 GLN cc_start: 0.7910 (mt0) cc_final: 0.7523 (mt0) REVERT: A 38 GLU cc_start: 0.8584 (tt0) cc_final: 0.8137 (tt0) REVERT: A 209 MET cc_start: 0.8399 (mtp) cc_final: 0.8121 (mtt) REVERT: A 344 MET cc_start: 0.7750 (tpt) cc_final: 0.7156 (tmm) REVERT: A 348 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: A 441 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7899 (mm-30) REVERT: A 461 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: A 466 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6065 (tt0) REVERT: A 491 ARG cc_start: 0.7725 (mmt180) cc_final: 0.6933 (mtm-85) REVERT: A 570 ILE cc_start: 0.6549 (mt) cc_final: 0.6346 (mm) REVERT: B 33 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7286 (mt-10) REVERT: B 85 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8110 (p0) REVERT: B 156 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7286 (ttp-110) REVERT: B 159 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6937 (mm-30) REVERT: B 165 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 241 LEU cc_start: 0.8315 (mt) cc_final: 0.8005 (tt) REVERT: B 264 ASP cc_start: 0.7638 (m-30) cc_final: 0.7332 (m-30) REVERT: B 325 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7524 (t0) REVERT: B 393 GLU cc_start: 0.6991 (tt0) cc_final: 0.6740 (tt0) REVERT: B 397 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7814 (mt0) REVERT: B 408 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7762 (tpp80) REVERT: B 525 GLU cc_start: 0.5964 (mt-10) cc_final: 0.5286 (tp30) REVERT: B 541 GLN cc_start: 0.5431 (mp10) cc_final: 0.4617 (mt0) REVERT: B 547 ARG cc_start: 0.5841 (mmm-85) cc_final: 0.5239 (mmt180) REVERT: B 550 ARG cc_start: 0.6087 (tpp-160) cc_final: 0.5655 (tpm170) REVERT: C 159 GLU cc_start: 0.7804 (pt0) cc_final: 0.7574 (pp20) REVERT: C 342 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7836 (mm-30) REVERT: C 375 GLU cc_start: 0.7764 (tt0) cc_final: 0.7221 (mt-10) REVERT: C 424 TRP cc_start: 0.7958 (p90) cc_final: 0.7616 (p-90) REVERT: C 480 GLU cc_start: 0.7520 (mp0) cc_final: 0.7006 (mm-30) REVERT: C 530 ILE cc_start: 0.7350 (mt) cc_final: 0.6976 (mt) REVERT: C 538 GLU cc_start: 0.6335 (mt-10) cc_final: 0.5484 (mm-30) REVERT: C 565 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6997 (mt-10) REVERT: C 571 GLN cc_start: 0.6537 (mp10) cc_final: 0.6288 (mt0) REVERT: D 39 THR cc_start: 0.7722 (p) cc_final: 0.7416 (t) REVERT: D 49 GLU cc_start: 0.7896 (tt0) cc_final: 0.7676 (tt0) REVERT: D 185 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6634 (mm-30) REVERT: D 338 GLN cc_start: 0.8426 (tt0) cc_final: 0.8221 (tp40) REVERT: D 406 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5670 (pm20) REVERT: D 416 ASP cc_start: 0.7963 (t0) cc_final: 0.7703 (t70) REVERT: D 421 PHE cc_start: 0.8235 (m-80) cc_final: 0.8007 (m-80) REVERT: D 452 LYS cc_start: 0.7778 (mmtp) cc_final: 0.7458 (mmtp) REVERT: E 81 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.8092 (mtt-85) REVERT: E 276 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.4879 (mp0) REVERT: E 321 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7656 (ttt-90) REVERT: E 353 ASP cc_start: 0.7961 (t0) cc_final: 0.7684 (t70) REVERT: E 376 LYS cc_start: 0.8168 (tttm) cc_final: 0.7730 (ttpt) REVERT: E 420 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7741 (mtm-85) REVERT: E 465 GLN cc_start: 0.6602 (tt0) cc_final: 0.6309 (mm110) REVERT: F 7 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8056 (mt-10) REVERT: F 9 THR cc_start: 0.8234 (m) cc_final: 0.7977 (p) REVERT: F 81 ARG cc_start: 0.8752 (mtt-85) cc_final: 0.8386 (mtt-85) REVERT: F 248 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7901 (mt-10) REVERT: F 437 GLN cc_start: 0.8361 (tt0) cc_final: 0.7781 (mm-40) REVERT: F 452 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7570 (mtmt) REVERT: G 155 LYS cc_start: 0.6018 (mttt) cc_final: 0.5427 (tptp) REVERT: G 164 LEU cc_start: 0.5555 (OUTLIER) cc_final: 0.5298 (tp) REVERT: H 1 MET cc_start: 0.2982 (pmm) cc_final: 0.2131 (tmt) REVERT: J 164 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5026 (tm-30) REVERT: J 170 ARG cc_start: 0.3362 (mtp85) cc_final: 0.3051 (mtp85) REVERT: L 82 GLU cc_start: 0.2740 (OUTLIER) cc_final: 0.2436 (mp0) REVERT: L 142 LEU cc_start: 0.3905 (pt) cc_final: 0.3616 (mt) REVERT: L 158 GLU cc_start: 0.4447 (mm-30) cc_final: 0.4227 (pm20) outliers start: 90 outliers final: 39 residues processed: 420 average time/residue: 0.8282 time to fit residues: 394.1946 Evaluate side-chains 338 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 49 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 270 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109258 restraints weight = 38510.063| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.80 r_work: 0.3015 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30114 Z= 0.154 Angle : 0.553 6.814 40813 Z= 0.286 Chirality : 0.044 0.169 4572 Planarity : 0.005 0.050 5333 Dihedral : 5.647 162.043 4199 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.95 % Allowed : 11.35 % Favored : 85.70 % 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: 0.77 (0.14), residues: 3764 helix: 1.53 (0.13), residues: 1567 sheet: 0.00 (0.22), residues: 559 loop : -0.22 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 460 TYR 0.014 0.001 TYR A 25 PHE 0.017 0.002 PHE C 574 TRP 0.017 0.001 TRP C 119 HIS 0.004 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (30114) covalent geometry : angle 0.55315 / 0.29 (40813) hydrogen bonds : bond 0.04907 / 3.31 ( 1274) hydrogen bonds : angle 4.68209 / 3.27 ( 3651) *********************** 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 407 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 316 time to evaluate : 1.210 Fit side-chains REVERT: A 3 GLN cc_start: 0.7809 (mt0) cc_final: 0.7436 (mt0) REVERT: A 38 GLU cc_start: 0.8515 (tt0) cc_final: 0.8067 (tt0) REVERT: A 93 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8291 (mmp80) REVERT: A 209 MET cc_start: 0.8334 (mtp) cc_final: 0.7992 (mtt) REVERT: A 343 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 344 MET cc_start: 0.7725 (tpt) cc_final: 0.7207 (tmm) REVERT: A 348 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: A 441 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 466 GLU cc_start: 0.6350 (mt-10) cc_final: 0.6043 (tt0) REVERT: A 491 ARG cc_start: 0.7714 (mmt180) cc_final: 0.6936 (mtm-85) REVERT: A 548 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6693 (tt) REVERT: B 85 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8056 (p0) REVERT: B 156 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7250 (ttp-110) REVERT: B 159 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6836 (mm-30) REVERT: B 165 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7329 (mm-30) REVERT: B 241 LEU cc_start: 0.8250 (mt) cc_final: 0.7986 (tt) REVERT: B 276 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6681 (mttp) REVERT: B 397 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7790 (mt0) REVERT: B 408 ARG cc_start: 0.7953 (ttm170) cc_final: 0.7702 (tpp80) REVERT: B 517 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.5811 (mmtm) REVERT: B 525 GLU cc_start: 0.5868 (mt-10) cc_final: 0.5352 (tp30) REVERT: B 541 GLN cc_start: 0.5408 (mp10) cc_final: 0.4633 (mt0) REVERT: B 547 ARG cc_start: 0.5750 (mmm-85) cc_final: 0.5003 (mmt180) REVERT: B 550 ARG cc_start: 0.6058 (tpp-160) cc_final: 0.5836 (tpm170) REVERT: C 122 MET cc_start: 0.7772 (mtp) cc_final: 0.7560 (mtp) REVERT: C 159 GLU cc_start: 0.7779 (pt0) cc_final: 0.7543 (pp20) REVERT: C 342 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7674 (mm-30) REVERT: C 375 GLU cc_start: 0.7719 (tt0) cc_final: 0.7157 (mt-10) REVERT: C 424 TRP cc_start: 0.7865 (p90) cc_final: 0.7533 (p-90) REVERT: C 456 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: C 480 GLU cc_start: 0.7374 (mp0) cc_final: 0.7001 (mp0) REVERT: C 530 ILE cc_start: 0.7322 (mt) cc_final: 0.6939 (mt) REVERT: C 565 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6667 (mt-10) REVERT: D 39 THR cc_start: 0.7712 (p) cc_final: 0.7451 (t) REVERT: D 49 GLU cc_start: 0.7799 (tt0) cc_final: 0.7565 (tt0) REVERT: D 185 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6647 (mm-30) REVERT: D 230 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7790 (mt-10) REVERT: D 338 GLN cc_start: 0.8367 (tt0) cc_final: 0.8135 (tp40) REVERT: D 406 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5606 (pm20) REVERT: D 421 PHE cc_start: 0.8216 (m-80) cc_final: 0.7986 (m-80) REVERT: D 452 LYS cc_start: 0.7747 (mmtp) cc_final: 0.7504 (mmtp) REVERT: E 81 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.8035 (mtt-85) REVERT: E 353 ASP cc_start: 0.7927 (t0) cc_final: 0.7677 (t70) REVERT: E 376 LYS cc_start: 0.8147 (tttm) cc_final: 0.7693 (ttpt) REVERT: E 420 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7639 (mtm-85) REVERT: E 427 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: E 465 GLN cc_start: 0.6558 (tt0) cc_final: 0.6245 (mm110) REVERT: F 7 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7950 (mt-10) REVERT: F 9 THR cc_start: 0.8114 (m) cc_final: 0.7789 (p) REVERT: F 81 ARG cc_start: 0.8700 (mtt-85) cc_final: 0.8326 (mtm180) REVERT: F 87 GLU cc_start: 0.7218 (pt0) cc_final: 0.6923 (pt0) REVERT: F 394 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7464 (pttm) REVERT: F 437 GLN cc_start: 0.8335 (tt0) cc_final: 0.7727 (mm-40) REVERT: F 452 LYS cc_start: 0.7952 (mmtp) cc_final: 0.7566 (mtmt) REVERT: G 155 LYS cc_start: 0.6049 (mttt) cc_final: 0.5425 (tptp) REVERT: G 197 ILE cc_start: 0.6789 (pt) cc_final: 0.6290 (mm) REVERT: H 1 MET cc_start: 0.2927 (pmm) cc_final: 0.2177 (tmt) REVERT: J 141 GLU cc_start: 0.3916 (OUTLIER) cc_final: 0.3434 (mt-10) REVERT: J 164 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.4816 (tm-30) REVERT: L 82 GLU cc_start: 0.2799 (OUTLIER) cc_final: 0.2539 (mp0) REVERT: L 158 GLU cc_start: 0.4427 (mm-30) cc_final: 0.4173 (pm20) outliers start: 91 outliers final: 42 residues processed: 382 average time/residue: 0.8592 time to fit residues: 372.9608 Evaluate side-chains 341 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 293 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 311 optimal weight: 0.0020 chunk 86 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 239 optimal weight: 7.9990 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109709 restraints weight = 38038.403| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.69 r_work: 0.2980 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30114 Z= 0.213 Angle : 0.631 8.075 40813 Z= 0.326 Chirality : 0.047 0.194 4572 Planarity : 0.006 0.054 5333 Dihedral : 5.922 174.312 4199 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.86 % Allowed : 12.91 % Favored : 83.23 % 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: 0.44 (0.14), residues: 3764 helix: 1.25 (0.13), residues: 1563 sheet: -0.08 (0.22), residues: 554 loop : -0.43 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 170 TYR 0.018 0.002 TYR A 25 PHE 0.024 0.002 PHE C 230 TRP 0.017 0.002 TRP C 119 HIS 0.011 0.002 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.21 (30114) covalent geometry : angle 0.63092 / 0.33 (40813) hydrogen bonds : bond 0.05599 / 3.76 ( 1274) hydrogen bonds : angle 4.81986 / 3.38 ( 3651) *********************** 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 414 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 295 time to evaluate : 1.168 Fit side-chains REVERT: A 3 GLN cc_start: 0.7904 (mt0) cc_final: 0.7471 (mt0) REVERT: A 38 GLU cc_start: 0.8542 (tt0) cc_final: 0.8128 (tt0) REVERT: A 93 ARG cc_start: 0.8544 (mmm160) cc_final: 0.8337 (mmp80) REVERT: A 209 MET cc_start: 0.8433 (mtp) cc_final: 0.8123 (mtt) REVERT: A 344 MET cc_start: 0.7789 (tpt) cc_final: 0.7225 (tmm) REVERT: A 348 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: A 441 GLU cc_start: 0.8212 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 461 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: A 466 GLU cc_start: 0.6397 (mt-10) cc_final: 0.6062 (tt0) REVERT: A 491 ARG cc_start: 0.7828 (mmt180) cc_final: 0.7094 (mtm-85) REVERT: A 548 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6875 (tt) REVERT: B 85 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8038 (p0) REVERT: B 92 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: B 156 ARG cc_start: 0.7617 (ttm170) cc_final: 0.7247 (ttp-110) REVERT: B 159 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6874 (mm-30) REVERT: B 165 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 170 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6831 (mm-30) REVERT: B 241 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8052 (tt) REVERT: B 276 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6016 (mmtt) REVERT: B 397 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7860 (mt0) REVERT: B 408 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7695 (tpp80) REVERT: B 541 GLN cc_start: 0.5416 (mp10) cc_final: 0.4657 (mt0) REVERT: B 547 ARG cc_start: 0.5833 (mmm-85) cc_final: 0.5055 (mmt180) REVERT: C 159 GLU cc_start: 0.7821 (pt0) cc_final: 0.7581 (pp20) REVERT: C 342 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7870 (mm-30) REVERT: C 375 GLU cc_start: 0.7812 (tt0) cc_final: 0.7246 (mt-10) REVERT: C 424 TRP cc_start: 0.7911 (p90) cc_final: 0.7588 (p-90) REVERT: C 456 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: C 480 GLU cc_start: 0.7414 (mp0) cc_final: 0.7079 (mp0) REVERT: C 530 ILE cc_start: 0.7376 (mt) cc_final: 0.7006 (mt) REVERT: C 565 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6710 (mt-10) REVERT: D 49 GLU cc_start: 0.7883 (tt0) cc_final: 0.7674 (tt0) REVERT: D 185 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6651 (mm-30) REVERT: D 287 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8549 (ttm) REVERT: D 406 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5666 (pm20) REVERT: D 421 PHE cc_start: 0.8252 (m-80) cc_final: 0.8030 (m-80) REVERT: D 452 LYS cc_start: 0.7834 (mmtp) cc_final: 0.7578 (mmtp) REVERT: E 141 MET cc_start: 0.8782 (mtp) cc_final: 0.8481 (mtp) REVERT: E 248 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: E 276 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5047 (mp0) REVERT: E 353 ASP cc_start: 0.7929 (t0) cc_final: 0.7683 (t70) REVERT: E 376 LYS cc_start: 0.8281 (tttm) cc_final: 0.7825 (ttpt) REVERT: E 398 ILE cc_start: 0.5646 (mm) cc_final: 0.5437 (pt) REVERT: E 405 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6416 (p) REVERT: E 420 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7852 (mtm-85) REVERT: E 427 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: E 465 GLN cc_start: 0.6741 (tt0) cc_final: 0.6227 (mm110) REVERT: F 7 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8075 (mt-10) REVERT: F 9 THR cc_start: 0.8234 (m) cc_final: 0.7901 (p) REVERT: F 81 ARG cc_start: 0.8773 (mtt-85) cc_final: 0.8410 (mtm180) REVERT: F 87 GLU cc_start: 0.7305 (pt0) cc_final: 0.7052 (pt0) REVERT: F 437 GLN cc_start: 0.8327 (tt0) cc_final: 0.7823 (mm-40) REVERT: F 452 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7600 (mtmt) REVERT: G 155 LYS cc_start: 0.6152 (mttt) cc_final: 0.5583 (tptp) REVERT: G 164 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5369 (tp) REVERT: H 1 MET cc_start: 0.3206 (pmm) cc_final: 0.2389 (tmt) REVERT: J 141 GLU cc_start: 0.3965 (OUTLIER) cc_final: 0.3486 (mt-10) REVERT: J 158 GLU cc_start: 0.4821 (tp30) cc_final: 0.4581 (mm-30) REVERT: J 164 GLU cc_start: 0.5829 (OUTLIER) cc_final: 0.4910 (tm-30) REVERT: L 82 GLU cc_start: 0.2836 (OUTLIER) cc_final: 0.2563 (mp0) outliers start: 119 outliers final: 56 residues processed: 385 average time/residue: 0.7921 time to fit residues: 348.0477 Evaluate side-chains 356 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 282 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 54 optimal weight: 0.0040 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN F 465 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110402 restraints weight = 38231.121| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.79 r_work: 0.3009 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30114 Z= 0.166 Angle : 0.566 7.198 40813 Z= 0.293 Chirality : 0.045 0.168 4572 Planarity : 0.005 0.082 5333 Dihedral : 5.469 128.893 4199 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.02 % Allowed : 13.88 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.13), residues: 1575 sheet: -0.10 (0.22), residues: 555 loop : -0.43 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 170 TYR 0.015 0.002 TYR A 25 PHE 0.018 0.002 PHE C 230 TRP 0.015 0.001 TRP J 100 HIS 0.010 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (30114) covalent geometry : angle 0.56587 / 0.29 (40813) hydrogen bonds : bond 0.04970 / 3.35 ( 1274) hydrogen bonds : angle 4.67631 / 3.27 ( 3651) *********************** 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 416 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 292 time to evaluate : 1.066 Fit side-chains REVERT: A 3 GLN cc_start: 0.7913 (mt0) cc_final: 0.7450 (mt0) REVERT: A 38 GLU cc_start: 0.8508 (tt0) cc_final: 0.8139 (tt0) REVERT: A 93 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8292 (mmp80) REVERT: A 344 MET cc_start: 0.7739 (tpt) cc_final: 0.7179 (tmm) REVERT: A 348 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: A 461 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: A 466 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6018 (tt0) REVERT: A 491 ARG cc_start: 0.7763 (mmt180) cc_final: 0.6992 (mtm-85) REVERT: A 548 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6690 (tt) REVERT: B 85 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 92 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: B 156 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7207 (ttp-110) REVERT: B 159 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6644 (mm-30) REVERT: B 165 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7261 (mm-30) REVERT: B 170 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6828 (mm-30) REVERT: B 241 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7992 (tt) REVERT: B 276 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6681 (mttp) REVERT: B 316 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: B 397 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7754 (mt0) REVERT: B 408 ARG cc_start: 0.7897 (ttm170) cc_final: 0.7650 (tpp80) REVERT: B 517 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.5899 (mmtm) REVERT: B 525 GLU cc_start: 0.6141 (mt-10) cc_final: 0.5560 (tp30) REVERT: B 541 GLN cc_start: 0.5427 (mp10) cc_final: 0.4653 (mt0) REVERT: B 547 ARG cc_start: 0.5795 (mmm-85) cc_final: 0.4998 (mmt180) REVERT: C 342 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7820 (mm-30) REVERT: C 375 GLU cc_start: 0.7734 (tt0) cc_final: 0.7164 (mt-10) REVERT: C 424 TRP cc_start: 0.7844 (p90) cc_final: 0.7541 (p-90) REVERT: C 456 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7513 (tp30) REVERT: C 480 GLU cc_start: 0.7365 (mp0) cc_final: 0.7047 (mp0) REVERT: C 530 ILE cc_start: 0.7333 (mt) cc_final: 0.7006 (mt) REVERT: C 565 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6705 (mt-10) REVERT: D 49 GLU cc_start: 0.7822 (tt0) cc_final: 0.7596 (tt0) REVERT: D 243 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: D 406 GLU cc_start: 0.5949 (mm-30) cc_final: 0.5598 (pm20) REVERT: D 452 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7615 (mmtp) REVERT: D 465 GLN cc_start: 0.7333 (pt0) cc_final: 0.7115 (pt0) REVERT: E 141 MET cc_start: 0.8729 (mtp) cc_final: 0.8469 (mtp) REVERT: E 248 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: E 353 ASP cc_start: 0.7909 (t0) cc_final: 0.7670 (t70) REVERT: E 376 LYS cc_start: 0.8214 (tttm) cc_final: 0.7885 (tttp) REVERT: E 380 ASP cc_start: 0.7810 (m-30) cc_final: 0.7510 (m-30) REVERT: E 398 ILE cc_start: 0.5763 (mm) cc_final: 0.5548 (pt) REVERT: E 405 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6353 (p) REVERT: E 420 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7772 (mtm-85) REVERT: E 427 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: E 433 GLU cc_start: 0.7643 (mp0) cc_final: 0.7371 (mp0) REVERT: E 465 GLN cc_start: 0.6739 (tt0) cc_final: 0.6192 (mm110) REVERT: F 7 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7986 (mt-10) REVERT: F 9 THR cc_start: 0.8180 (m) cc_final: 0.7812 (p) REVERT: F 81 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.8353 (mtm180) REVERT: F 162 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: F 210 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7819 (ttp-110) REVERT: F 265 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: F 391 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7787 (t0) REVERT: F 437 GLN cc_start: 0.8397 (tt0) cc_final: 0.7817 (mm-40) REVERT: F 452 LYS cc_start: 0.8061 (mmtp) cc_final: 0.7566 (mtmt) REVERT: G 155 LYS cc_start: 0.6204 (mttt) cc_final: 0.5357 (tppt) REVERT: G 164 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5186 (tp) REVERT: H 1 MET cc_start: 0.3059 (pmm) cc_final: 0.2512 (tmt) REVERT: H 93 LEU cc_start: 0.3665 (OUTLIER) cc_final: 0.3410 (pp) REVERT: J 141 GLU cc_start: 0.4029 (OUTLIER) cc_final: 0.3624 (mt-10) REVERT: J 158 GLU cc_start: 0.4835 (tp30) cc_final: 0.4628 (mm-30) REVERT: J 164 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5078 (tm-30) REVERT: L 82 GLU cc_start: 0.2967 (OUTLIER) cc_final: 0.2664 (mp0) outliers start: 124 outliers final: 59 residues processed: 388 average time/residue: 0.7835 time to fit residues: 346.3869 Evaluate side-chains 362 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 279 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 158 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 253 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 361 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN F 465 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110251 restraints weight = 38107.703| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.80 r_work: 0.3001 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30114 Z= 0.180 Angle : 0.591 9.872 40813 Z= 0.304 Chirality : 0.046 0.188 4572 Planarity : 0.005 0.054 5333 Dihedral : 5.448 113.290 4199 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.80 % Allowed : 14.79 % Favored : 81.41 % 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: 0.42 (0.14), residues: 3764 helix: 1.27 (0.13), residues: 1580 sheet: -0.13 (0.22), residues: 555 loop : -0.48 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 550 TYR 0.016 0.002 TYR A 25 PHE 0.020 0.002 PHE C 230 TRP 0.015 0.002 TRP J 100 HIS 0.012 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (30114) covalent geometry : angle 0.59107 / 0.30 (40813) hydrogen bonds : bond 0.05159 / 3.47 ( 1274) hydrogen bonds : angle 4.72008 / 3.31 ( 3651) *********************** 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 396 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 279 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7916 (mt0) cc_final: 0.7435 (mt0) REVERT: A 38 GLU cc_start: 0.8510 (tt0) cc_final: 0.8155 (tt0) REVERT: A 93 ARG cc_start: 0.8496 (mmm160) cc_final: 0.8255 (mmp80) REVERT: A 344 MET cc_start: 0.7746 (tpt) cc_final: 0.7166 (tmm) REVERT: A 348 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 461 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: A 466 GLU cc_start: 0.6386 (mt-10) cc_final: 0.6014 (tt0) REVERT: A 491 ARG cc_start: 0.7772 (mmt180) cc_final: 0.6973 (mtm-85) REVERT: A 548 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6646 (tt) REVERT: B 85 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8021 (p0) REVERT: B 92 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: B 156 ARG cc_start: 0.7558 (ttm170) cc_final: 0.7143 (ttp-110) REVERT: B 159 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6670 (mm-30) REVERT: B 165 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 241 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7979 (tt) REVERT: B 276 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6704 (mttp) REVERT: B 316 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: B 397 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7769 (mt0) REVERT: B 408 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7645 (tpp80) REVERT: B 517 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.5875 (mmtm) REVERT: B 525 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5521 (tp30) REVERT: B 547 ARG cc_start: 0.5692 (mmm-85) cc_final: 0.4878 (mmt180) REVERT: C 342 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7824 (mm-30) REVERT: C 375 GLU cc_start: 0.7742 (tt0) cc_final: 0.7198 (mt-10) REVERT: C 456 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: C 480 GLU cc_start: 0.7354 (mp0) cc_final: 0.7039 (mp0) REVERT: C 530 ILE cc_start: 0.7348 (mt) cc_final: 0.7035 (mt) REVERT: C 565 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6577 (mt-10) REVERT: D 49 GLU cc_start: 0.7816 (tt0) cc_final: 0.7592 (tt0) REVERT: D 243 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: D 406 GLU cc_start: 0.5931 (mm-30) cc_final: 0.5562 (pm20) REVERT: D 452 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7603 (mmtp) REVERT: E 141 MET cc_start: 0.8768 (mtp) cc_final: 0.8425 (mtp) REVERT: E 248 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: E 353 ASP cc_start: 0.7900 (t0) cc_final: 0.7653 (t70) REVERT: E 376 LYS cc_start: 0.8238 (tttm) cc_final: 0.7979 (tttp) REVERT: E 405 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6392 (p) REVERT: E 420 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7787 (mtm-85) REVERT: E 427 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: E 433 GLU cc_start: 0.7657 (mp0) cc_final: 0.7368 (mp0) REVERT: E 465 GLN cc_start: 0.6816 (tt0) cc_final: 0.6214 (mm110) REVERT: F 7 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7974 (mt-10) REVERT: F 9 THR cc_start: 0.8187 (m) cc_final: 0.7825 (p) REVERT: F 81 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.8447 (mtm180) REVERT: F 207 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7576 (mm-30) REVERT: F 210 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7816 (ttp-110) REVERT: F 265 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: F 437 GLN cc_start: 0.8381 (tt0) cc_final: 0.7795 (mm-40) REVERT: G 22 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6710 (tt0) REVERT: G 155 LYS cc_start: 0.6097 (mttt) cc_final: 0.5330 (tppt) REVERT: G 164 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5224 (tp) REVERT: H 1 MET cc_start: 0.2953 (pmm) cc_final: 0.2485 (tmt) REVERT: J 81 GLU cc_start: 0.2266 (OUTLIER) cc_final: 0.1906 (pt0) REVERT: J 141 GLU cc_start: 0.4092 (OUTLIER) cc_final: 0.3648 (mt-10) REVERT: J 158 GLU cc_start: 0.4915 (tp30) cc_final: 0.4614 (mm-30) REVERT: J 164 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5028 (tm-30) REVERT: L 82 GLU cc_start: 0.2936 (OUTLIER) cc_final: 0.2672 (mp0) REVERT: L 150 LEU cc_start: 0.2172 (OUTLIER) cc_final: 0.1829 (pp) outliers start: 117 outliers final: 62 residues processed: 372 average time/residue: 0.7703 time to fit residues: 327.7155 Evaluate side-chains 357 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 272 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 303 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 208 optimal weight: 8.9990 chunk 371 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111938 restraints weight = 38116.247| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.79 r_work: 0.2992 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30114 Z= 0.223 Angle : 0.645 15.108 40813 Z= 0.332 Chirality : 0.048 0.201 4572 Planarity : 0.006 0.055 5333 Dihedral : 5.640 112.332 4199 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.99 % Allowed : 15.02 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3764 helix: 1.12 (0.13), residues: 1562 sheet: -0.19 (0.22), residues: 555 loop : -0.58 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 170 TYR 0.018 0.002 TYR B 25 PHE 0.024 0.002 PHE C 230 TRP 0.016 0.002 TRP J 100 HIS 0.014 0.002 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.22 (30114) covalent geometry : angle 0.64480 / 0.33 (40813) hydrogen bonds : bond 0.05687 / 3.82 ( 1274) hydrogen bonds : angle 4.86429 / 3.41 ( 3651) *********************** 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 402 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 279 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7937 (mt0) cc_final: 0.7436 (mt0) REVERT: A 38 GLU cc_start: 0.8503 (tt0) cc_final: 0.8127 (tt0) REVERT: A 93 ARG cc_start: 0.8506 (mmm160) cc_final: 0.8256 (mmp80) REVERT: A 344 MET cc_start: 0.7760 (tpt) cc_final: 0.7170 (tmm) REVERT: A 348 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: A 461 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: A 466 GLU cc_start: 0.6378 (mt-10) cc_final: 0.6020 (tt0) REVERT: A 491 ARG cc_start: 0.7806 (mmt180) cc_final: 0.6993 (mtm-85) REVERT: A 548 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6732 (tt) REVERT: B 85 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8016 (p0) REVERT: B 92 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 156 ARG cc_start: 0.7464 (ttm170) cc_final: 0.7078 (ttp-110) REVERT: B 159 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6745 (mm-30) REVERT: B 165 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 241 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8019 (tt) REVERT: B 276 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6055 (mmtt) REVERT: B 397 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7789 (mt0) REVERT: B 408 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7670 (tpp80) REVERT: B 517 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.5798 (mmtm) REVERT: B 525 GLU cc_start: 0.6165 (mt-10) cc_final: 0.5525 (tp30) REVERT: B 547 ARG cc_start: 0.5654 (mmm-85) cc_final: 0.4883 (mmt180) REVERT: C 182 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8103 (mtmm) REVERT: C 342 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7918 (mm-30) REVERT: C 375 GLU cc_start: 0.7791 (tt0) cc_final: 0.7230 (mt-10) REVERT: C 456 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: C 480 GLU cc_start: 0.7095 (mp0) cc_final: 0.6781 (mp0) REVERT: C 481 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6967 (tpp80) REVERT: C 530 ILE cc_start: 0.7393 (mt) cc_final: 0.7068 (mt) REVERT: D 34 ASP cc_start: 0.7673 (p0) cc_final: 0.7407 (p0) REVERT: D 49 GLU cc_start: 0.7836 (tt0) cc_final: 0.7627 (tt0) REVERT: D 243 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: D 287 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8512 (ttm) REVERT: D 406 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5621 (pm20) REVERT: D 452 LYS cc_start: 0.7901 (mmtp) cc_final: 0.7637 (mmtp) REVERT: E 128 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: E 141 MET cc_start: 0.8778 (mtp) cc_final: 0.8467 (mtp) REVERT: E 248 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: E 353 ASP cc_start: 0.7909 (t0) cc_final: 0.7651 (t70) REVERT: E 376 LYS cc_start: 0.8290 (tttm) cc_final: 0.8017 (tttm) REVERT: E 405 THR cc_start: 0.6737 (OUTLIER) cc_final: 0.6299 (p) REVERT: E 420 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7826 (mtm-85) REVERT: E 427 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: F 7 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8113 (mt-10) REVERT: F 9 THR cc_start: 0.8243 (m) cc_final: 0.7885 (p) REVERT: F 25 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7838 (pttt) REVERT: F 34 ASP cc_start: 0.7817 (m-30) cc_final: 0.7570 (p0) REVERT: F 81 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.8468 (mtm180) REVERT: F 87 GLU cc_start: 0.7326 (pt0) cc_final: 0.7042 (pt0) REVERT: F 162 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: F 207 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7573 (mm-30) REVERT: F 210 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7838 (ttp-110) REVERT: F 265 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: F 437 GLN cc_start: 0.8382 (tt0) cc_final: 0.7812 (mm-40) REVERT: G 155 LYS cc_start: 0.6133 (mttt) cc_final: 0.5365 (tppt) REVERT: G 164 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5267 (tp) REVERT: H 1 MET cc_start: 0.3189 (pmm) cc_final: 0.2705 (tmt) REVERT: J 81 GLU cc_start: 0.2601 (OUTLIER) cc_final: 0.2205 (pt0) REVERT: J 141 GLU cc_start: 0.4083 (OUTLIER) cc_final: 0.3656 (mt-10) REVERT: J 158 GLU cc_start: 0.4867 (tp30) cc_final: 0.4561 (mm-30) REVERT: J 164 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.4990 (tm-30) REVERT: L 82 GLU cc_start: 0.2812 (OUTLIER) cc_final: 0.2565 (mp0) outliers start: 123 outliers final: 73 residues processed: 380 average time/residue: 0.7788 time to fit residues: 338.4067 Evaluate side-chains 368 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 269 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 316 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 330 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 347 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN L 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111215 restraints weight = 38273.188| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.66 r_work: 0.3003 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30114 Z= 0.145 Angle : 0.557 10.541 40813 Z= 0.286 Chirality : 0.044 0.165 4572 Planarity : 0.005 0.069 5333 Dihedral : 5.357 107.006 4199 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.57 % Allowed : 15.63 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3764 helix: 1.30 (0.13), residues: 1590 sheet: -0.10 (0.22), residues: 561 loop : -0.48 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 460 TYR 0.012 0.001 TYR A 25 PHE 0.018 0.001 PHE A 230 TRP 0.017 0.001 TRP J 100 HIS 0.008 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (30114) covalent geometry : angle 0.55737 / 0.29 (40813) hydrogen bonds : bond 0.04748 / 3.21 ( 1274) hydrogen bonds : angle 4.65534 / 3.26 ( 3651) *********************** 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 395 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 285 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7953 (mt0) cc_final: 0.7470 (mt0) REVERT: A 38 GLU cc_start: 0.8472 (tt0) cc_final: 0.8162 (tt0) REVERT: A 93 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8269 (mmp80) REVERT: A 156 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6936 (ttm-80) REVERT: A 344 MET cc_start: 0.7735 (tpt) cc_final: 0.7191 (tmm) REVERT: A 348 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 466 GLU cc_start: 0.6246 (mt-10) cc_final: 0.5928 (tt0) REVERT: A 548 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6645 (tt) REVERT: B 85 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8019 (p0) REVERT: B 92 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 156 ARG cc_start: 0.7503 (ttm170) cc_final: 0.7095 (ttp-110) REVERT: B 159 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6727 (mm-30) REVERT: B 165 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7328 (mm-30) REVERT: B 241 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8004 (tt) REVERT: B 276 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6738 (mttp) REVERT: B 316 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: B 397 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7799 (mt0) REVERT: B 408 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7668 (tpp80) REVERT: B 525 GLU cc_start: 0.6176 (mt-10) cc_final: 0.5615 (tp30) REVERT: B 547 ARG cc_start: 0.5704 (mmm-85) cc_final: 0.4930 (mmt180) REVERT: C 342 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7875 (mm-30) REVERT: C 375 GLU cc_start: 0.7818 (tt0) cc_final: 0.7245 (mt-10) REVERT: C 456 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: C 480 GLU cc_start: 0.7172 (mp0) cc_final: 0.6900 (mp0) REVERT: C 530 ILE cc_start: 0.7332 (mt) cc_final: 0.6966 (mt) REVERT: D 243 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: D 287 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8509 (ttm) REVERT: D 406 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5568 (pm20) REVERT: D 452 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7621 (mmtp) REVERT: D 465 GLN cc_start: 0.7219 (pt0) cc_final: 0.6960 (pt0) REVERT: E 141 MET cc_start: 0.8708 (mtp) cc_final: 0.8415 (mtp) REVERT: E 248 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: E 353 ASP cc_start: 0.7942 (t0) cc_final: 0.7686 (t70) REVERT: E 376 LYS cc_start: 0.8226 (tttm) cc_final: 0.7922 (tttm) REVERT: E 380 ASP cc_start: 0.7871 (m-30) cc_final: 0.7552 (m-30) REVERT: E 405 THR cc_start: 0.6816 (OUTLIER) cc_final: 0.6418 (p) REVERT: E 420 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7805 (mtm-85) REVERT: E 427 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: F 7 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8080 (mt-10) REVERT: F 9 THR cc_start: 0.8155 (m) cc_final: 0.7780 (p) REVERT: F 25 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7579 (pttp) REVERT: F 34 ASP cc_start: 0.7853 (m-30) cc_final: 0.7614 (p0) REVERT: F 81 ARG cc_start: 0.8716 (mtt-85) cc_final: 0.8477 (mtm180) REVERT: F 162 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: F 265 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: F 437 GLN cc_start: 0.8414 (tt0) cc_final: 0.7809 (mm-40) REVERT: G 155 LYS cc_start: 0.6048 (mttt) cc_final: 0.5364 (tppt) REVERT: G 164 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5214 (tp) REVERT: H 1 MET cc_start: 0.3301 (pmm) cc_final: 0.2768 (tmt) REVERT: J 81 GLU cc_start: 0.2500 (OUTLIER) cc_final: 0.2214 (pt0) REVERT: J 141 GLU cc_start: 0.3865 (OUTLIER) cc_final: 0.3568 (mt-10) REVERT: J 158 GLU cc_start: 0.4815 (tp30) cc_final: 0.4512 (mm-30) REVERT: J 164 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.4888 (tm-30) outliers start: 110 outliers final: 60 residues processed: 372 average time/residue: 0.7685 time to fit residues: 326.8721 Evaluate side-chains 364 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 283 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 371 optimal weight: 0.9980 chunk 370 optimal weight: 20.0000 chunk 203 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN E 310 GLN F 437 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113302 restraints weight = 38271.081| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.78 r_work: 0.3071 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30114 Z= 0.102 Angle : 0.495 10.695 40813 Z= 0.252 Chirality : 0.042 0.162 4572 Planarity : 0.004 0.053 5333 Dihedral : 4.873 91.928 4199 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.24 % Allowed : 17.13 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3764 helix: 1.66 (0.13), residues: 1583 sheet: 0.03 (0.22), residues: 565 loop : -0.25 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 170 TYR 0.009 0.001 TYR E 13 PHE 0.018 0.001 PHE A 230 TRP 0.016 0.001 TRP C 119 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (30114) covalent geometry : angle 0.49514 / 0.25 (40813) hydrogen bonds : bond 0.03669 / 2.51 ( 1274) hydrogen bonds : angle 4.36328 / 3.05 ( 3651) *********************** 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 377 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 308 time to evaluate : 1.143 Fit side-chains REVERT: A 3 GLN cc_start: 0.7887 (mt0) cc_final: 0.7406 (mt0) REVERT: A 38 GLU cc_start: 0.8363 (tt0) cc_final: 0.7998 (tt0) REVERT: A 343 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 344 MET cc_start: 0.7655 (tpt) cc_final: 0.7427 (tpt) REVERT: A 348 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: A 466 GLU cc_start: 0.6206 (mt-10) cc_final: 0.5863 (tt0) REVERT: B 85 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7933 (p0) REVERT: B 92 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: B 156 ARG cc_start: 0.7359 (ttm170) cc_final: 0.6953 (ttp-110) REVERT: B 159 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6724 (mm-30) REVERT: B 165 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 276 LYS cc_start: 0.7017 (mttp) cc_final: 0.6130 (ttpp) REVERT: B 397 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7696 (mt0) REVERT: B 408 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7615 (tpp80) REVERT: B 460 ARG cc_start: 0.6707 (mtp180) cc_final: 0.6413 (mtp180) REVERT: B 525 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5807 (tp30) REVERT: B 547 ARG cc_start: 0.5684 (mmm-85) cc_final: 0.4811 (mmt180) REVERT: C 342 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7601 (mm-30) REVERT: C 375 GLU cc_start: 0.7678 (tt0) cc_final: 0.7138 (mt-10) REVERT: C 424 TRP cc_start: 0.7754 (p90) cc_final: 0.7469 (p-90) REVERT: C 456 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: C 480 GLU cc_start: 0.7283 (mp0) cc_final: 0.6981 (mp0) REVERT: C 530 ILE cc_start: 0.7282 (mt) cc_final: 0.6945 (mt) REVERT: D 316 MET cc_start: 0.7730 (mtm) cc_final: 0.7086 (mtp) REVERT: D 406 GLU cc_start: 0.5830 (mm-30) cc_final: 0.5581 (pm20) REVERT: D 452 LYS cc_start: 0.7898 (mmtp) cc_final: 0.7614 (mmtp) REVERT: E 248 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: E 353 ASP cc_start: 0.7849 (t0) cc_final: 0.7596 (t70) REVERT: E 376 LYS cc_start: 0.8128 (tttm) cc_final: 0.7839 (tttt) REVERT: E 380 ASP cc_start: 0.7669 (m-30) cc_final: 0.7364 (m-30) REVERT: E 405 THR cc_start: 0.6842 (OUTLIER) cc_final: 0.6447 (p) REVERT: E 420 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7780 (mtm-85) REVERT: E 427 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: E 457 ASP cc_start: 0.8056 (p0) cc_final: 0.7846 (p0) REVERT: F 7 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7885 (mm-30) REVERT: F 9 THR cc_start: 0.7912 (m) cc_final: 0.7513 (p) REVERT: F 25 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7535 (pttp) REVERT: F 81 ARG cc_start: 0.8645 (mtt-85) cc_final: 0.8354 (mtm180) REVERT: F 87 GLU cc_start: 0.7145 (pt0) cc_final: 0.6936 (pt0) REVERT: F 437 GLN cc_start: 0.8328 (tt0) cc_final: 0.7740 (mm-40) REVERT: F 457 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6480 (t0) REVERT: G 10 ASN cc_start: 0.7571 (m-40) cc_final: 0.7329 (m-40) REVERT: G 155 LYS cc_start: 0.6133 (mttt) cc_final: 0.5375 (tppt) REVERT: G 197 ILE cc_start: 0.6704 (pt) cc_final: 0.6434 (mm) REVERT: H 1 MET cc_start: 0.3121 (pmm) cc_final: 0.2630 (tmt) REVERT: J 137 GLU cc_start: 0.3579 (tt0) cc_final: 0.3011 (mm-30) REVERT: J 141 GLU cc_start: 0.4041 (OUTLIER) cc_final: 0.3785 (mt-10) REVERT: J 158 GLU cc_start: 0.4857 (tp30) cc_final: 0.4555 (mm-30) REVERT: L 141 GLU cc_start: 0.3029 (tp30) cc_final: 0.2455 (tt0) outliers start: 69 outliers final: 34 residues processed: 366 average time/residue: 0.8201 time to fit residues: 342.4518 Evaluate side-chains 331 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 295 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 288 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 325 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 chunk 286 optimal weight: 0.0670 chunk 250 optimal weight: 0.7980 chunk 219 optimal weight: 0.3980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN F 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116284 restraints weight = 38271.205| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.72 r_work: 0.3079 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30114 Z= 0.098 Angle : 0.495 10.240 40813 Z= 0.251 Chirality : 0.042 0.151 4572 Planarity : 0.004 0.071 5333 Dihedral : 4.715 89.732 4199 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.62 % Allowed : 17.97 % Favored : 80.41 % 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: 1.03 (0.14), residues: 3764 helix: 1.78 (0.13), residues: 1585 sheet: 0.17 (0.23), residues: 562 loop : -0.16 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG A 460 TYR 0.010 0.001 TYR D 331 PHE 0.018 0.001 PHE C 574 TRP 0.015 0.001 TRP J 100 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (30114) covalent geometry : angle 0.49518 / 0.25 (40813) hydrogen bonds : bond 0.03516 / 2.41 ( 1274) hydrogen bonds : angle 4.27494 / 2.98 ( 3651) ********************** 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 344 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 1.198 Fit side-chains REVERT: A 3 GLN cc_start: 0.7912 (mt0) cc_final: 0.7431 (mt0) REVERT: A 38 GLU cc_start: 0.8355 (tt0) cc_final: 0.7976 (tt0) REVERT: A 343 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 344 MET cc_start: 0.7653 (tpt) cc_final: 0.7403 (tpt) REVERT: A 348 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: A 570 ILE cc_start: 0.6139 (mm) cc_final: 0.5931 (mt) REVERT: B 85 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7963 (p0) REVERT: B 92 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: B 156 ARG cc_start: 0.7401 (ttm170) cc_final: 0.6979 (ttp-110) REVERT: B 159 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6744 (mm-30) REVERT: B 165 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 276 LYS cc_start: 0.7010 (mttp) cc_final: 0.6145 (ttpp) REVERT: B 397 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7655 (mt0) REVERT: B 460 ARG cc_start: 0.6656 (mtp180) cc_final: 0.6384 (mtp180) REVERT: B 525 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5730 (tp30) REVERT: B 547 ARG cc_start: 0.5662 (mmm-85) cc_final: 0.4921 (mmt180) REVERT: C 342 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7605 (mm-30) REVERT: C 375 GLU cc_start: 0.7744 (tt0) cc_final: 0.7209 (mt-10) REVERT: C 410 ASP cc_start: 0.8437 (t0) cc_final: 0.8208 (t70) REVERT: C 424 TRP cc_start: 0.7696 (p90) cc_final: 0.7450 (p-90) REVERT: C 456 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7470 (tp30) REVERT: C 480 GLU cc_start: 0.7213 (mp0) cc_final: 0.7008 (mp0) REVERT: C 530 ILE cc_start: 0.7401 (mt) cc_final: 0.7042 (mt) REVERT: C 532 ARG cc_start: 0.6578 (ptp90) cc_final: 0.6203 (tmm-80) REVERT: D 316 MET cc_start: 0.7680 (mtm) cc_final: 0.7122 (mtp) REVERT: D 406 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5662 (pm20) REVERT: D 452 LYS cc_start: 0.7890 (mmtp) cc_final: 0.7554 (mttp) REVERT: E 248 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: E 353 ASP cc_start: 0.7925 (t0) cc_final: 0.7705 (t70) REVERT: E 376 LYS cc_start: 0.8121 (tttm) cc_final: 0.7859 (tttt) REVERT: E 380 ASP cc_start: 0.7703 (m-30) cc_final: 0.7341 (m-30) REVERT: E 405 THR cc_start: 0.6888 (OUTLIER) cc_final: 0.6479 (p) REVERT: E 420 ARG cc_start: 0.8032 (mtm110) cc_final: 0.7786 (mtm-85) REVERT: E 427 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: E 465 GLN cc_start: 0.6673 (tt0) cc_final: 0.6204 (mm110) REVERT: F 7 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7870 (mm-30) REVERT: F 9 THR cc_start: 0.7932 (m) cc_final: 0.7537 (p) REVERT: F 81 ARG cc_start: 0.8649 (mtt-85) cc_final: 0.8362 (mtm180) REVERT: F 437 GLN cc_start: 0.8333 (tt0) cc_final: 0.7731 (mm-40) REVERT: F 457 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6469 (t0) REVERT: G 10 ASN cc_start: 0.7528 (m-40) cc_final: 0.7283 (m-40) REVERT: G 155 LYS cc_start: 0.6039 (mttt) cc_final: 0.5386 (tppt) REVERT: G 197 ILE cc_start: 0.6765 (pt) cc_final: 0.6416 (mm) REVERT: H 1 MET cc_start: 0.3110 (pmm) cc_final: 0.2618 (tmt) REVERT: J 137 GLU cc_start: 0.3689 (tt0) cc_final: 0.3120 (mm-30) REVERT: J 141 GLU cc_start: 0.4106 (OUTLIER) cc_final: 0.3803 (mt-10) REVERT: J 158 GLU cc_start: 0.4839 (tp30) cc_final: 0.4559 (mm-30) REVERT: L 141 GLU cc_start: 0.3260 (tp30) cc_final: 0.2640 (tt0) outliers start: 50 outliers final: 33 residues processed: 336 average time/residue: 0.8494 time to fit residues: 326.1227 Evaluate side-chains 330 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 31 optimal weight: 6.9990 chunk 361 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 367 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 181 optimal weight: 0.1980 chunk 226 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN F 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112610 restraints weight = 38055.953| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.77 r_work: 0.2998 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30114 Z= 0.178 Angle : 0.596 11.400 40813 Z= 0.304 Chirality : 0.046 0.166 4572 Planarity : 0.005 0.053 5333 Dihedral : 5.230 94.632 4199 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 17.71 % Favored : 80.15 % 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: 0.66 (0.14), residues: 3764 helix: 1.46 (0.13), residues: 1583 sheet: 0.03 (0.22), residues: 561 loop : -0.36 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 170 TYR 0.017 0.002 TYR B 25 PHE 0.022 0.002 PHE C 230 TRP 0.014 0.002 TRP J 100 HIS 0.011 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (30114) covalent geometry : angle 0.59556 / 0.30 (40813) hydrogen bonds : bond 0.04964 / 3.35 ( 1274) hydrogen bonds : angle 4.56367 / 3.19 ( 3651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10635.38 seconds wall clock time: 181 minutes 18.56 seconds (10878.56 seconds total)