Starting phenix.real_space_refine on Tue Apr 7 16:18:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vav_31866/04_2026/7vav_31866.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vav_31866/04_2026/7vav_31866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vav_31866/04_2026/7vav_31866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vav_31866/04_2026/7vav_31866.map" model { file = "/net/cci-nas-00/data/ceres_data/7vav_31866/04_2026/7vav_31866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vav_31866/04_2026/7vav_31866.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 5 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18720 2.51 5 N 5125 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29520 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4467 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} 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: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} 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: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 981 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 7.03, per 1000 atoms: 0.24 Number of scatterers: 29520 At special positions: 0 Unit cell: (139.04, 176.88, 154, 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 5 15.00 Mg 2 11.99 O 5565 8.00 N 5125 7.00 C 18720 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: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6916 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 25 sheets defined 47.8% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 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: 4.074A 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: 4.308A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.130A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.613A pdb=" N ASP A 390 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.842A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.603A 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 541 removed outlier: 3.525A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.673A 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 575 removed outlier: 3.680A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.686A 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 244 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.645A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.714A 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: 3.722A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.595A pdb=" N ALA B 475 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.848A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 558 through 578 removed outlier: 3.660A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (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: 3.999A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.390A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 342 Processing helix chain 'C' and resid 353 through 364 removed outlier: 3.848A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.530A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.546A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.292A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.686A 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 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.708A 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: 3.719A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.533A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 removed outlier: 3.576A pdb=" N MET D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.874A 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: 3.672A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.536A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.593A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.629A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.286A 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 445 through 446 No H-bonds generated for 'chain 'D' and resid 445 through 446' Processing helix chain 'D' and resid 447 through 451 removed outlier: 3.724A pdb=" N LEU D 451 " --> pdb=" O GLN D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.922A 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 removed outlier: 3.580A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.899A 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: 4.004A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.776A 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 275 removed outlier: 3.859A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.550A 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 366 removed outlier: 3.511A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 361 through 366' Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.929A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 445 through 446 No H-bonds generated for 'chain 'E' and resid 445 through 446' Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 457 through 462 removed outlier: 4.033A pdb=" N LYS E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.540A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.666A 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 135 through 140 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.522A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) 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 227 through 232 removed outlier: 3.676A pdb=" N ARG F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 275 removed outlier: 4.034A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.628A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 374 through 399 Processing helix chain 'F' and resid 400 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 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.760A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.630A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 removed outlier: 3.892A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.894A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 208 removed outlier: 3.594A pdb=" N GLY G 171 " --> pdb=" O VAL G 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 25 through 40 Processing helix chain 'H' and resid 54 through 58 Processing helix chain 'H' and resid 59 through 64 removed outlier: 4.309A pdb=" N ARG H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 85 through 99 removed outlier: 3.801A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 105 removed outlier: 3.965A pdb=" N TYR I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.542A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 removed outlier: 3.761A pdb=" N LEU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.574A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 130 Processing helix chain 'J' and resid 131 through 138 Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.290A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 84 through 105 removed outlier: 4.035A pdb=" N TYR K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 127 through 139 removed outlier: 4.547A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.779A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.623A 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: 6.472A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.086A 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: 5.613A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.749A 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: 5.986A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 50 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: 5.834A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.588A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (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: 5.750A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.540A 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: 5.685A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 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: 6.449A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.720A 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 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 145 removed outlier: 5.720A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.538A 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: 6.982A 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 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 148 removed outlier: 6.338A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.976A 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: 3.871A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 6 through 8 removed outlier: 5.665A pdb=" N THR J 161 " --> pdb=" O GLY J 156 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA J 120 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.712A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.160A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.810A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 93 removed outlier: 8.611A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.491A 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: 3.635A 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 93 removed outlier: 3.588A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLN F 336 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LEU F 355 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN F 338 " --> pdb=" O ASP F 353 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.685A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.694A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.410A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1326 hydrogen bonds defined for protein. 3783 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: 5.86 Time building geometry restraints manager: 3.37 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: 9941 1.34 - 1.46: 3778 1.46 - 1.57: 16152 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30074 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.592 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C8 ADP A 601 " pdb=" N7 ADP A 601 " ideal model delta sigma weight residual 1.350 1.310 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C5 ADP A 601 " pdb=" N7 ADP A 601 " ideal model delta sigma weight residual 1.350 1.387 -0.037 2.00e-02 2.50e+03 3.41e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 40672 3.25 - 6.50: 72 6.50 - 9.75: 8 9.75 - 13.00: 1 13.00 - 16.25: 1 Bond angle restraints: 40754 Sorted by residual: angle pdb=" PA ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 120.50 136.75 -16.25 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O2B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 119.90 107.25 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" C GLY G 118 " pdb=" N THR G 119 " pdb=" CA THR G 119 " ideal model delta sigma weight residual 120.06 124.95 -4.89 1.19e+00 7.06e-01 1.69e+01 angle pdb=" C GLY D 116 " pdb=" N LEU D 117 " pdb=" CA LEU D 117 " ideal model delta sigma weight residual 120.49 126.23 -5.74 1.42e+00 4.96e-01 1.63e+01 angle pdb=" C1' ADP A 601 " pdb=" C2' ADP A 601 " pdb=" C3' ADP A 601 " ideal model delta sigma weight residual 111.00 101.48 9.52 3.00e+00 1.11e-01 1.01e+01 ... (remaining 40749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.47: 17826 29.47 - 58.93: 446 58.93 - 88.40: 70 88.40 - 117.87: 6 117.87 - 147.33: 1 Dihedral angle restraints: 18349 sinusoidal: 7531 harmonic: 10818 Sorted by residual: dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 87.33 -147.33 1 2.00e+01 2.50e-03 4.42e+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 -164.27 104.27 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" CA ASP D 416 " pdb=" CB ASP D 416 " pdb=" CG ASP D 416 " pdb=" OD1 ASP D 416 " ideal model delta sinusoidal sigma weight residual -30.00 -88.50 58.50 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 18346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3137 0.034 - 0.068: 936 0.068 - 0.102: 335 0.102 - 0.136: 156 0.136 - 0.171: 3 Chirality restraints: 4567 Sorted by residual: 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 -2.68 0.17 2.00e-01 2.50e+01 7.27e-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 2.50 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CB THR D 107 " pdb=" CA THR D 107 " pdb=" OG1 THR D 107 " pdb=" CG2 THR D 107 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 4564 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 124 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO L 125 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 125 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 125 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 229 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO D 324 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 216 2.61 - 3.18: 24743 3.18 - 3.75: 44828 3.75 - 4.33: 61985 4.33 - 4.90: 105779 Nonbonded interactions: 237551 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 2.035 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.059 2.170 nonbonded pdb=" O2B ADP A 601 " pdb="MG MG A 602 " model vdw 2.103 2.170 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLU H 28 " model vdw 2.147 3.040 nonbonded pdb=" O LEU B 241 " pdb=" OG SER B 245 " model vdw 2.182 3.040 ... (remaining 237546 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 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 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: 6.150 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: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 27.590 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.002 0.104 30074 Z= 0.117 Angle : 0.495 16.247 40754 Z= 0.258 Chirality : 0.041 0.171 4567 Planarity : 0.004 0.046 5336 Dihedral : 13.378 147.334 11433 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.14), residues: 3761 helix: 2.25 (0.14), residues: 1547 sheet: 0.49 (0.22), residues: 583 loop : 0.56 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.009 0.001 TYR E 383 PHE 0.014 0.001 PHE G 108 TRP 0.010 0.001 TRP F 471 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00237 (30074) covalent geometry : angle 0.49466 (40754) hydrogen bonds : bond 0.15720 ( 1326) hydrogen bonds : angle 5.87467 ( 3783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7583 (m-70) cc_final: 0.7290 (m-70) REVERT: A 166 TYR cc_start: 0.7948 (m-80) cc_final: 0.7585 (m-80) REVERT: A 180 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6074 (mm-30) REVERT: A 282 MET cc_start: 0.8076 (tpt) cc_final: 0.7833 (tpt) REVERT: A 391 MET cc_start: 0.8057 (mmt) cc_final: 0.7638 (mmt) REVERT: A 416 ARG cc_start: 0.7453 (ttm110) cc_final: 0.7089 (mtp-110) REVERT: A 441 GLU cc_start: 0.7765 (tp30) cc_final: 0.7471 (mp0) REVERT: A 481 ARG cc_start: 0.6053 (tpt-90) cc_final: 0.5634 (mtm180) REVERT: A 531 LYS cc_start: 0.6641 (mttm) cc_final: 0.6276 (mmmm) REVERT: A 538 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 567 MET cc_start: 0.6765 (mmm) cc_final: 0.6478 (mmp) REVERT: B 127 ASP cc_start: 0.6910 (m-30) cc_final: 0.6706 (m-30) REVERT: B 144 THR cc_start: 0.8332 (m) cc_final: 0.7981 (t) REVERT: B 156 ARG cc_start: 0.6224 (ptm-80) cc_final: 0.5740 (ptp90) REVERT: B 176 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6705 (mt-10) REVERT: B 445 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7021 (tm-30) REVERT: B 455 SER cc_start: 0.6904 (t) cc_final: 0.6538 (m) REVERT: B 496 GLN cc_start: 0.7958 (tt0) cc_final: 0.7748 (mt0) REVERT: C 124 LYS cc_start: 0.7177 (mppt) cc_final: 0.6728 (mppt) REVERT: C 127 ASP cc_start: 0.7112 (m-30) cc_final: 0.6784 (m-30) REVERT: C 170 GLU cc_start: 0.7763 (tp30) cc_final: 0.7525 (tp30) REVERT: C 179 THR cc_start: 0.7558 (m) cc_final: 0.7194 (p) REVERT: C 220 MET cc_start: 0.7694 (mmt) cc_final: 0.7455 (tpt) REVERT: C 276 LYS cc_start: 0.7227 (mtpt) cc_final: 0.6965 (mmmm) REVERT: C 391 MET cc_start: 0.8439 (mmt) cc_final: 0.8146 (mmt) REVERT: C 478 ASP cc_start: 0.6258 (m-30) cc_final: 0.5947 (m-30) REVERT: C 525 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6096 (mt-10) REVERT: C 546 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6294 (tt0) REVERT: C 571 GLN cc_start: 0.6518 (pp30) cc_final: 0.6186 (tp40) REVERT: D 67 ASP cc_start: 0.7556 (p0) cc_final: 0.7251 (p0) REVERT: D 280 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7296 (mtp85) REVERT: D 452 LYS cc_start: 0.7899 (mttp) cc_final: 0.7606 (mmpt) REVERT: E 26 ASP cc_start: 0.7772 (m-30) cc_final: 0.7332 (t0) REVERT: E 136 SER cc_start: 0.8528 (m) cc_final: 0.8245 (t) REVERT: E 175 PRO cc_start: 0.7063 (Cg_endo) cc_final: 0.6817 (Cg_exo) REVERT: E 413 GLN cc_start: 0.5154 (pt0) cc_final: 0.4933 (tp40) REVERT: E 437 GLN cc_start: 0.7613 (tt0) cc_final: 0.7318 (tm-30) REVERT: F 15 SER cc_start: 0.8373 (t) cc_final: 0.7955 (p) REVERT: F 98 LYS cc_start: 0.7689 (mmtm) cc_final: 0.7239 (ttpp) REVERT: F 210 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6696 (mtm110) REVERT: F 230 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7559 (mt-10) REVERT: F 296 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7841 (mm-30) REVERT: F 362 MET cc_start: 0.8361 (ttt) cc_final: 0.8137 (ttp) REVERT: G 92 GLU cc_start: 0.2111 (mt-10) cc_final: 0.1463 (mp0) REVERT: G 152 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7394 (pp20) REVERT: G 185 GLN cc_start: 0.7155 (tp40) cc_final: 0.6939 (tp40) REVERT: G 200 LYS cc_start: 0.6508 (mttp) cc_final: 0.6272 (mmmt) REVERT: J 141 GLU cc_start: 0.6112 (tt0) cc_final: 0.5751 (tp30) REVERT: J 160 LYS cc_start: 0.7158 (mmtp) cc_final: 0.6912 (mtmt) REVERT: J 173 ARG cc_start: 0.4744 (ttm-80) cc_final: 0.3540 (ttp80) REVERT: L 145 GLU cc_start: 0.4229 (tp30) cc_final: 0.3818 (mt-10) outliers start: 0 outliers final: 0 residues processed: 581 average time/residue: 0.9654 time to fit residues: 629.7651 Evaluate side-chains 291 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 8.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 3 GLN B 469 GLN D 206 GLN F 166 GLN F 170 GLN F 413 GLN G 180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.135192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103266 restraints weight = 50961.100| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.25 r_work: 0.3367 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30074 Z= 0.189 Angle : 0.593 10.672 40754 Z= 0.306 Chirality : 0.046 0.191 4567 Planarity : 0.005 0.053 5336 Dihedral : 5.524 117.386 4230 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.43 % Allowed : 9.05 % Favored : 88.51 % 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: 1.38 (0.14), residues: 3761 helix: 1.88 (0.14), residues: 1560 sheet: 0.30 (0.23), residues: 565 loop : 0.31 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 547 TYR 0.012 0.002 TYR G 133 PHE 0.019 0.002 PHE C 559 TRP 0.015 0.001 TRP B 119 HIS 0.008 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00452 (30074) covalent geometry : angle 0.59292 (40754) hydrogen bonds : bond 0.05070 ( 1326) hydrogen bonds : angle 4.83046 ( 3783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.8128 (m-70) cc_final: 0.7835 (m-70) REVERT: A 122 MET cc_start: 0.7790 (mtp) cc_final: 0.7420 (mtt) REVERT: A 180 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6438 (mm-30) REVERT: A 220 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8228 (ttp) REVERT: A 282 MET cc_start: 0.8346 (tpt) cc_final: 0.8088 (tpt) REVERT: A 391 MET cc_start: 0.8356 (mmt) cc_final: 0.8064 (mmt) REVERT: A 441 GLU cc_start: 0.8494 (tp30) cc_final: 0.8064 (mp0) REVERT: A 481 ARG cc_start: 0.6752 (tpt-90) cc_final: 0.6202 (mtm180) REVERT: A 538 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 567 MET cc_start: 0.7417 (mmm) cc_final: 0.7106 (mmp) REVERT: B 143 PHE cc_start: 0.7514 (m-80) cc_final: 0.7233 (m-80) REVERT: B 156 ARG cc_start: 0.7152 (ptm-80) cc_final: 0.6601 (ptp90) REVERT: B 176 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7210 (mt-10) REVERT: B 340 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7235 (ttm-80) REVERT: B 445 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7245 (tm-30) REVERT: B 455 SER cc_start: 0.7745 (t) cc_final: 0.7421 (m) REVERT: B 459 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7536 (mm110) REVERT: B 496 GLN cc_start: 0.8575 (tt0) cc_final: 0.8333 (mt0) REVERT: B 550 ARG cc_start: 0.7235 (tpt90) cc_final: 0.6944 (tpp80) REVERT: C 124 LYS cc_start: 0.7488 (mppt) cc_final: 0.6936 (mptt) REVERT: C 127 ASP cc_start: 0.7878 (m-30) cc_final: 0.7240 (m-30) REVERT: C 133 MET cc_start: 0.8422 (mtp) cc_final: 0.8027 (mtp) REVERT: C 157 VAL cc_start: 0.7912 (t) cc_final: 0.7630 (p) REVERT: C 169 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7878 (mm-30) REVERT: C 344 MET cc_start: 0.8633 (ttm) cc_final: 0.8326 (ttp) REVERT: C 478 ASP cc_start: 0.6517 (m-30) cc_final: 0.6204 (m-30) REVERT: C 525 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7006 (mt-10) REVERT: C 546 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6708 (tm-30) REVERT: C 558 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6936 (pt0) REVERT: D 265 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: D 280 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7841 (mtp-110) REVERT: D 452 LYS cc_start: 0.8145 (mttp) cc_final: 0.7932 (mmtt) REVERT: E 26 ASP cc_start: 0.8228 (m-30) cc_final: 0.7761 (t0) REVERT: E 175 PRO cc_start: 0.7057 (Cg_endo) cc_final: 0.6765 (Cg_exo) REVERT: E 210 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7003 (ttp80) REVERT: E 305 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8098 (mptp) REVERT: E 407 ASN cc_start: 0.6541 (OUTLIER) cc_final: 0.6326 (t0) REVERT: E 437 GLN cc_start: 0.7862 (tt0) cc_final: 0.7569 (tm-30) REVERT: F 98 LYS cc_start: 0.8330 (mmtm) cc_final: 0.7993 (ttpp) REVERT: G 152 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7484 (pp20) REVERT: J 153 ARG cc_start: 0.4371 (OUTLIER) cc_final: 0.4022 (tmm160) REVERT: J 173 ARG cc_start: 0.4885 (ttm-80) cc_final: 0.3666 (ttp80) REVERT: L 142 LEU cc_start: 0.6794 (pt) cc_final: 0.6563 (pt) REVERT: L 145 GLU cc_start: 0.4080 (tp30) cc_final: 0.3482 (mt-10) REVERT: L 168 LEU cc_start: 0.5751 (mt) cc_final: 0.5314 (tm) outliers start: 75 outliers final: 20 residues processed: 347 average time/residue: 0.8927 time to fit residues: 352.4604 Evaluate side-chains 265 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 220 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN E 262 ASN E 407 ASN F 166 GLN G 180 GLN ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 162 GLN L 143 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.132165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100813 restraints weight = 51420.374| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.01 r_work: 0.3386 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30074 Z= 0.208 Angle : 0.595 8.549 40754 Z= 0.308 Chirality : 0.046 0.235 4567 Planarity : 0.005 0.056 5336 Dihedral : 5.475 87.514 4230 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.89 % Allowed : 11.52 % Favored : 85.59 % 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: 0.98 (0.14), residues: 3761 helix: 1.65 (0.13), residues: 1562 sheet: 0.06 (0.22), residues: 557 loop : -0.03 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 416 TYR 0.019 0.002 TYR G 133 PHE 0.019 0.002 PHE C 559 TRP 0.016 0.002 TRP B 119 HIS 0.011 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00503 (30074) covalent geometry : angle 0.59484 (40754) hydrogen bonds : bond 0.05212 ( 1326) hydrogen bonds : angle 4.79627 ( 3783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 244 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.7922 (m-70) cc_final: 0.7672 (m-70) REVERT: A 122 MET cc_start: 0.7860 (mtp) cc_final: 0.7122 (tmm) REVERT: A 180 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6516 (mm-30) REVERT: A 441 GLU cc_start: 0.8442 (tp30) cc_final: 0.8029 (mp0) REVERT: A 481 ARG cc_start: 0.6829 (tpt-90) cc_final: 0.6271 (mtm110) REVERT: A 538 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7060 (mt-10) REVERT: B 156 ARG cc_start: 0.7230 (ptm-80) cc_final: 0.6961 (ptp-170) REVERT: B 165 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: B 176 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7488 (mt-10) REVERT: B 262 MET cc_start: 0.8490 (mmm) cc_final: 0.8156 (tpt) REVERT: B 340 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7274 (ttm-80) REVERT: B 436 ASP cc_start: 0.6797 (m-30) cc_final: 0.6573 (m-30) REVERT: B 445 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7228 (tm-30) REVERT: B 455 SER cc_start: 0.7764 (t) cc_final: 0.7411 (m) REVERT: B 459 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7558 (mm110) REVERT: B 496 GLN cc_start: 0.8664 (tt0) cc_final: 0.8238 (tp40) REVERT: B 550 ARG cc_start: 0.7169 (tpt90) cc_final: 0.6910 (tpt90) REVERT: C 124 LYS cc_start: 0.7595 (mppt) cc_final: 0.7049 (mptt) REVERT: C 127 ASP cc_start: 0.8176 (m-30) cc_final: 0.7762 (m-30) REVERT: C 133 MET cc_start: 0.8408 (mtp) cc_final: 0.8038 (mtp) REVERT: C 156 ARG cc_start: 0.6729 (ttm170) cc_final: 0.6239 (ttm-80) REVERT: C 157 VAL cc_start: 0.7886 (t) cc_final: 0.7592 (p) REVERT: C 169 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7848 (mm-30) REVERT: C 170 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: C 336 GLU cc_start: 0.8249 (tp30) cc_final: 0.7826 (tp30) REVERT: C 525 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7086 (mt-10) REVERT: C 546 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6756 (tm-30) REVERT: C 558 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7012 (pt0) REVERT: D 265 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: D 280 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7881 (mtp-110) REVERT: E 26 ASP cc_start: 0.8170 (m-30) cc_final: 0.7745 (t0) REVERT: E 175 PRO cc_start: 0.7291 (Cg_endo) cc_final: 0.6984 (Cg_exo) REVERT: E 210 ARG cc_start: 0.7371 (ttp80) cc_final: 0.7082 (ttm110) REVERT: E 305 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8007 (mptp) REVERT: E 382 LEU cc_start: 0.7681 (mp) cc_final: 0.7452 (mp) REVERT: E 437 GLN cc_start: 0.7843 (tt0) cc_final: 0.7580 (tm-30) REVERT: E 442 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6645 (pt) REVERT: F 98 LYS cc_start: 0.8370 (mmtm) cc_final: 0.7991 (ttpp) REVERT: G 159 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7061 (ptm160) REVERT: G 200 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6408 (tmtt) REVERT: H 1 MET cc_start: 0.1879 (OUTLIER) cc_final: -0.0487 (ppp) REVERT: I 104 MET cc_start: 0.1081 (mmp) cc_final: 0.0677 (ptt) REVERT: J 173 ARG cc_start: 0.5107 (ttm-80) cc_final: 0.3848 (ttp80) REVERT: L 168 LEU cc_start: 0.5881 (mt) cc_final: 0.5350 (tm) outliers start: 89 outliers final: 30 residues processed: 306 average time/residue: 0.8606 time to fit residues: 300.0332 Evaluate side-chains 253 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 140 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 330 optimal weight: 20.0000 chunk 326 optimal weight: 9.9990 chunk 284 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 364 optimal weight: 0.0270 chunk 165 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 368 optimal weight: 6.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 407 ASN E 407 ASN G 180 GLN H 84 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.101865 restraints weight = 50702.575| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.00 r_work: 0.3393 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30074 Z= 0.135 Angle : 0.527 12.185 40754 Z= 0.270 Chirality : 0.043 0.202 4567 Planarity : 0.005 0.058 5336 Dihedral : 5.199 88.234 4230 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.53 % Allowed : 12.98 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.14), residues: 3761 helix: 1.83 (0.14), residues: 1559 sheet: 0.02 (0.22), residues: 558 loop : -0.02 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 547 TYR 0.017 0.001 TYR G 133 PHE 0.015 0.001 PHE C 559 TRP 0.014 0.001 TRP B 119 HIS 0.007 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00316 (30074) covalent geometry : angle 0.52693 (40754) hydrogen bonds : bond 0.04402 ( 1326) hydrogen bonds : angle 4.60523 ( 3783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 246 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7471 (tmt90) REVERT: A 109 HIS cc_start: 0.7872 (m-70) cc_final: 0.7640 (m-70) REVERT: A 122 MET cc_start: 0.7852 (mtp) cc_final: 0.7033 (tmm) REVERT: A 180 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6893 (mp0) REVERT: A 220 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8258 (ttp) REVERT: A 441 GLU cc_start: 0.8407 (tp30) cc_final: 0.8005 (mp0) REVERT: A 481 ARG cc_start: 0.6783 (tpt-90) cc_final: 0.6269 (mtm180) REVERT: A 520 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 538 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 567 MET cc_start: 0.7323 (mmm) cc_final: 0.7047 (mmp) REVERT: B 156 ARG cc_start: 0.7226 (ptm-80) cc_final: 0.6919 (ptp-170) REVERT: B 165 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: B 176 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 262 MET cc_start: 0.8430 (mmm) cc_final: 0.8192 (tpt) REVERT: B 340 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7261 (ttm-80) REVERT: B 436 ASP cc_start: 0.6780 (m-30) cc_final: 0.6563 (m-30) REVERT: B 445 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7217 (tm-30) REVERT: B 455 SER cc_start: 0.7730 (t) cc_final: 0.7432 (m) REVERT: B 496 GLN cc_start: 0.8623 (tt0) cc_final: 0.8165 (tp40) REVERT: B 516 MET cc_start: 0.6719 (mtp) cc_final: 0.6391 (mtm) REVERT: B 550 ARG cc_start: 0.7122 (tpt90) cc_final: 0.6850 (tpt90) REVERT: C 124 LYS cc_start: 0.7581 (mppt) cc_final: 0.7120 (mppt) REVERT: C 127 ASP cc_start: 0.8110 (m-30) cc_final: 0.7789 (m-30) REVERT: C 133 MET cc_start: 0.8386 (mtp) cc_final: 0.8040 (mtp) REVERT: C 156 ARG cc_start: 0.6735 (ttm170) cc_final: 0.6291 (ttm-80) REVERT: C 169 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7859 (mm-30) REVERT: C 336 GLU cc_start: 0.8177 (tp30) cc_final: 0.7756 (tp30) REVERT: C 524 LYS cc_start: 0.7983 (mmpt) cc_final: 0.7533 (tmmt) REVERT: C 546 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6750 (tm-30) REVERT: C 558 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7055 (pt0) REVERT: D 265 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: D 280 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7814 (mtp-110) REVERT: D 407 ASN cc_start: 0.6006 (t0) cc_final: 0.5657 (t0) REVERT: E 26 ASP cc_start: 0.8165 (m-30) cc_final: 0.7806 (t0) REVERT: E 210 ARG cc_start: 0.7347 (ttp80) cc_final: 0.7114 (ttm170) REVERT: E 305 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8016 (mptp) REVERT: E 394 LYS cc_start: 0.6672 (tptp) cc_final: 0.6306 (mmmm) REVERT: E 437 GLN cc_start: 0.7896 (tt0) cc_final: 0.7599 (tm-30) REVERT: E 442 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6587 (pt) REVERT: F 98 LYS cc_start: 0.8362 (mmtm) cc_final: 0.7906 (ttpp) REVERT: G 159 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6967 (ptm160) REVERT: G 189 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: G 200 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6654 (mmmt) REVERT: H 1 MET cc_start: 0.1760 (mtt) cc_final: -0.0515 (ppp) REVERT: I 104 MET cc_start: 0.1100 (mmp) cc_final: 0.0701 (ptt) REVERT: J 110 GLU cc_start: 0.5197 (tp30) cc_final: 0.4755 (mm-30) REVERT: J 113 GLU cc_start: 0.4809 (OUTLIER) cc_final: 0.4287 (pp20) REVERT: J 153 ARG cc_start: 0.4398 (OUTLIER) cc_final: 0.4152 (tmm160) REVERT: J 161 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7603 (t) REVERT: J 173 ARG cc_start: 0.5045 (ttm-80) cc_final: 0.3809 (ttp80) REVERT: L 168 LEU cc_start: 0.5859 (mt) cc_final: 0.5382 (tm) outliers start: 78 outliers final: 32 residues processed: 303 average time/residue: 0.8760 time to fit residues: 302.9154 Evaluate side-chains 268 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain J residue 161 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 100 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 286 optimal weight: 0.1980 chunk 204 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN B 477 GLN E 338 GLN E 407 ASN G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.130727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099621 restraints weight = 51565.867| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.02 r_work: 0.3348 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 30074 Z= 0.277 Angle : 0.666 10.958 40754 Z= 0.344 Chirality : 0.048 0.203 4567 Planarity : 0.006 0.068 5336 Dihedral : 5.668 88.253 4230 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.50 % Allowed : 13.47 % Favored : 83.03 % 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: 0.49 (0.14), residues: 3761 helix: 1.35 (0.13), residues: 1555 sheet: -0.26 (0.22), residues: 559 loop : -0.36 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 314 TYR 0.024 0.002 TYR G 133 PHE 0.022 0.002 PHE C 559 TRP 0.018 0.002 TRP B 119 HIS 0.011 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00679 (30074) covalent geometry : angle 0.66637 (40754) hydrogen bonds : bond 0.05658 ( 1326) hydrogen bonds : angle 4.89536 ( 3783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 235 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7431 (tmt90) REVERT: A 109 HIS cc_start: 0.7925 (m-70) cc_final: 0.7697 (m-70) REVERT: A 122 MET cc_start: 0.7874 (mtp) cc_final: 0.7141 (tmm) REVERT: A 156 ARG cc_start: 0.7701 (ttt180) cc_final: 0.7495 (ttt-90) REVERT: A 180 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6856 (mm-30) REVERT: A 241 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8973 (mm) REVERT: A 257 GLU cc_start: 0.7448 (tp30) cc_final: 0.7070 (mm-30) REVERT: A 441 GLU cc_start: 0.8473 (tp30) cc_final: 0.8040 (mp0) REVERT: A 481 ARG cc_start: 0.6982 (tpt-90) cc_final: 0.6367 (mtm110) REVERT: A 520 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 531 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6879 (mtmm) REVERT: A 538 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 156 ARG cc_start: 0.7370 (ptm-80) cc_final: 0.7120 (ptp-170) REVERT: B 165 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: B 176 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7519 (mt-10) REVERT: B 262 MET cc_start: 0.8520 (mmm) cc_final: 0.8300 (tpt) REVERT: B 340 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7367 (ttm-80) REVERT: B 436 ASP cc_start: 0.6819 (m-30) cc_final: 0.6597 (m-30) REVERT: B 445 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7379 (tm-30) REVERT: B 459 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7462 (mm110) REVERT: B 460 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7032 (ttp80) REVERT: B 496 GLN cc_start: 0.8731 (tt0) cc_final: 0.8257 (tp40) REVERT: C 124 LYS cc_start: 0.7748 (mppt) cc_final: 0.7273 (mptt) REVERT: C 127 ASP cc_start: 0.8329 (m-30) cc_final: 0.8047 (m-30) REVERT: C 133 MET cc_start: 0.8476 (mtp) cc_final: 0.8251 (mtp) REVERT: C 156 ARG cc_start: 0.6871 (ttm170) cc_final: 0.6493 (ttm-80) REVERT: C 169 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7909 (mm-30) REVERT: C 336 GLU cc_start: 0.8299 (tp30) cc_final: 0.7851 (tp30) REVERT: C 524 LYS cc_start: 0.8021 (mmpt) cc_final: 0.7586 (tmmt) REVERT: C 546 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6780 (tm-30) REVERT: C 565 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6471 (tt0) REVERT: D 185 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5683 (mm-30) REVERT: D 237 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8757 (mtp) REVERT: D 265 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: D 280 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7852 (mtp-110) REVERT: D 287 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8538 (ttt) REVERT: D 388 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7905 (m-40) REVERT: D 420 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7088 (mpp-170) REVERT: E 7 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: E 26 ASP cc_start: 0.8311 (m-30) cc_final: 0.7729 (t0) REVERT: E 210 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7221 (ttm110) REVERT: E 305 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (mptp) REVERT: E 394 LYS cc_start: 0.6596 (tptp) cc_final: 0.6260 (mmmm) REVERT: E 437 GLN cc_start: 0.7852 (tt0) cc_final: 0.7541 (tm-30) REVERT: E 442 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6546 (pt) REVERT: G 159 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7022 (ptm160) REVERT: G 196 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6885 (ttm-80) REVERT: G 200 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6344 (tmtt) REVERT: G 201 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6294 (mp) REVERT: H 1 MET cc_start: 0.1978 (mtt) cc_final: -0.0587 (ppp) REVERT: I 104 MET cc_start: 0.1082 (mmp) cc_final: 0.0750 (ptt) REVERT: J 153 ARG cc_start: 0.4571 (OUTLIER) cc_final: 0.4310 (tmm160) REVERT: J 161 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7693 (t) REVERT: L 143 GLN cc_start: 0.6141 (mt0) cc_final: 0.5595 (mp10) REVERT: L 168 LEU cc_start: 0.6032 (mt) cc_final: 0.5542 (tm) outliers start: 108 outliers final: 46 residues processed: 318 average time/residue: 0.8446 time to fit residues: 307.7774 Evaluate side-chains 288 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 338 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 227 optimal weight: 0.0030 chunk 4 optimal weight: 0.9980 chunk 371 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 181 optimal weight: 0.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN F 170 GLN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.102439 restraints weight = 50832.213| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.02 r_work: 0.3397 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 30074 Z= 0.107 Angle : 0.512 11.334 40754 Z= 0.261 Chirality : 0.042 0.185 4567 Planarity : 0.004 0.062 5336 Dihedral : 5.102 84.692 4230 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.30 % Allowed : 15.25 % Favored : 82.45 % 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: 0.96 (0.14), residues: 3761 helix: 1.81 (0.14), residues: 1556 sheet: -0.13 (0.22), residues: 550 loop : -0.15 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 547 TYR 0.016 0.001 TYR G 133 PHE 0.011 0.001 PHE C 559 TRP 0.014 0.001 TRP B 119 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00230 (30074) covalent geometry : angle 0.51191 (40754) hydrogen bonds : bond 0.04049 ( 1326) hydrogen bonds : angle 4.53605 ( 3783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 243 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6293 (mtt) REVERT: A 95 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7434 (tmt90) REVERT: A 109 HIS cc_start: 0.7878 (m-70) cc_final: 0.7647 (m-70) REVERT: A 122 MET cc_start: 0.7786 (mtp) cc_final: 0.7059 (tmm) REVERT: A 156 ARG cc_start: 0.7730 (ttt180) cc_final: 0.7527 (ttt-90) REVERT: A 180 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7051 (mp0) REVERT: A 257 GLU cc_start: 0.7341 (tp30) cc_final: 0.6918 (mm-30) REVERT: A 441 GLU cc_start: 0.8420 (tp30) cc_final: 0.8016 (mp0) REVERT: A 481 ARG cc_start: 0.6831 (tpt-90) cc_final: 0.6281 (mtm180) REVERT: A 520 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8151 (mp) REVERT: B 156 ARG cc_start: 0.7196 (ptm-80) cc_final: 0.6843 (ptp-170) REVERT: B 165 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: B 176 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 340 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7141 (ttm-80) REVERT: B 436 ASP cc_start: 0.6840 (m-30) cc_final: 0.6607 (m-30) REVERT: B 445 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7333 (tm-30) REVERT: B 459 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7428 (mm110) REVERT: B 460 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7085 (ttp80) REVERT: B 496 GLN cc_start: 0.8689 (tt0) cc_final: 0.8246 (tp40) REVERT: B 516 MET cc_start: 0.6742 (mtp) cc_final: 0.6400 (mtm) REVERT: B 550 ARG cc_start: 0.7080 (tpt90) cc_final: 0.6735 (tpt90) REVERT: C 124 LYS cc_start: 0.7731 (mppt) cc_final: 0.7149 (mptt) REVERT: C 127 ASP cc_start: 0.8216 (m-30) cc_final: 0.7803 (m-30) REVERT: C 133 MET cc_start: 0.8348 (mtp) cc_final: 0.8127 (mtp) REVERT: C 156 ARG cc_start: 0.6790 (ttm170) cc_final: 0.6484 (ttm-80) REVERT: C 169 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 336 GLU cc_start: 0.8271 (tp30) cc_final: 0.7835 (tp30) REVERT: C 478 ASP cc_start: 0.6427 (m-30) cc_final: 0.5968 (m-30) REVERT: C 524 LYS cc_start: 0.8022 (mmpt) cc_final: 0.7578 (tmmt) REVERT: C 546 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6637 (tm-30) REVERT: D 265 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: D 280 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7822 (mtp-110) REVERT: D 296 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8332 (mm-30) REVERT: D 420 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7620 (tpp-160) REVERT: E 26 ASP cc_start: 0.8212 (m-30) cc_final: 0.7755 (t0) REVERT: E 210 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7151 (ttm170) REVERT: E 305 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8013 (mptp) REVERT: E 394 LYS cc_start: 0.6526 (tptp) cc_final: 0.6194 (mmmm) REVERT: E 437 GLN cc_start: 0.7837 (tt0) cc_final: 0.7544 (tm-30) REVERT: G 148 LYS cc_start: 0.6267 (mmmt) cc_final: 0.5975 (tppt) REVERT: G 159 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7027 (ptm160) REVERT: G 196 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6839 (ttm-80) REVERT: G 200 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6592 (mmmt) REVERT: G 201 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6213 (mp) REVERT: H 1 MET cc_start: 0.1371 (mtt) cc_final: -0.0525 (ppp) REVERT: I 104 MET cc_start: 0.1008 (mmp) cc_final: 0.0677 (ptt) REVERT: J 110 GLU cc_start: 0.5362 (tp30) cc_final: 0.4786 (mm-30) REVERT: J 153 ARG cc_start: 0.4450 (OUTLIER) cc_final: 0.4190 (tmm160) REVERT: J 173 ARG cc_start: 0.5119 (ttm-80) cc_final: 0.3870 (ttp80) REVERT: L 143 GLN cc_start: 0.6009 (mt0) cc_final: 0.5549 (mp10) REVERT: L 168 LEU cc_start: 0.5926 (mt) cc_final: 0.5473 (tm) outliers start: 71 outliers final: 28 residues processed: 295 average time/residue: 0.8454 time to fit residues: 285.0052 Evaluate side-chains 265 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain J residue 153 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 75 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN E 407 ASN F 166 GLN F 170 GLN G 180 GLN G 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.132807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101508 restraints weight = 51359.819| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.04 r_work: 0.3371 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30074 Z= 0.186 Angle : 0.574 10.842 40754 Z= 0.293 Chirality : 0.045 0.200 4567 Planarity : 0.005 0.062 5336 Dihedral : 5.239 85.115 4230 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.82 % Allowed : 15.31 % Favored : 81.86 % 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: 0.78 (0.14), residues: 3761 helix: 1.67 (0.14), residues: 1560 sheet: -0.22 (0.22), residues: 559 loop : -0.27 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 105 TYR 0.018 0.001 TYR G 133 PHE 0.018 0.002 PHE C 559 TRP 0.015 0.001 TRP B 119 HIS 0.007 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00453 (30074) covalent geometry : angle 0.57422 (40754) hydrogen bonds : bond 0.04713 ( 1326) hydrogen bonds : angle 4.64863 ( 3783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 227 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6411 (mtt) REVERT: A 95 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7436 (tmt90) REVERT: A 109 HIS cc_start: 0.7913 (m-70) cc_final: 0.7685 (m-70) REVERT: A 122 MET cc_start: 0.7845 (mtp) cc_final: 0.7077 (tmm) REVERT: A 156 ARG cc_start: 0.7759 (ttt180) cc_final: 0.7551 (ttt-90) REVERT: A 180 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6893 (mp0) REVERT: A 220 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8359 (ttp) REVERT: A 257 GLU cc_start: 0.7377 (tp30) cc_final: 0.6973 (mm-30) REVERT: A 441 GLU cc_start: 0.8477 (tp30) cc_final: 0.8045 (mp0) REVERT: A 481 ARG cc_start: 0.6897 (tpt-90) cc_final: 0.6354 (mtm110) REVERT: A 520 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 156 ARG cc_start: 0.7258 (ptm-80) cc_final: 0.6889 (ptp-170) REVERT: B 165 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: B 176 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7316 (mt-10) REVERT: B 340 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7303 (ttm-80) REVERT: B 436 ASP cc_start: 0.6877 (m-30) cc_final: 0.6658 (m-30) REVERT: B 459 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7451 (mm110) REVERT: B 460 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7022 (ttp80) REVERT: B 496 GLN cc_start: 0.8693 (tt0) cc_final: 0.8264 (tp40) REVERT: B 516 MET cc_start: 0.6728 (mtp) cc_final: 0.6354 (mtm) REVERT: B 550 ARG cc_start: 0.7156 (tpt90) cc_final: 0.6907 (tpt90) REVERT: C 124 LYS cc_start: 0.7803 (mppt) cc_final: 0.7250 (mptt) REVERT: C 127 ASP cc_start: 0.8294 (m-30) cc_final: 0.7915 (m-30) REVERT: C 133 MET cc_start: 0.8411 (mtp) cc_final: 0.8208 (mtp) REVERT: C 169 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7911 (mm-30) REVERT: C 170 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: C 336 GLU cc_start: 0.8292 (tp30) cc_final: 0.7844 (tp30) REVERT: C 478 ASP cc_start: 0.6505 (m-30) cc_final: 0.6060 (m-30) REVERT: C 524 LYS cc_start: 0.8034 (mmpt) cc_final: 0.7619 (tmmt) REVERT: C 546 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6685 (tm-30) REVERT: D 265 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: D 280 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7853 (mtp-110) REVERT: D 296 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8390 (mm-30) REVERT: D 420 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7672 (tpp-160) REVERT: E 26 ASP cc_start: 0.8279 (m-30) cc_final: 0.7752 (t0) REVERT: E 210 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7206 (ttm170) REVERT: E 305 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8074 (mptp) REVERT: E 394 LYS cc_start: 0.6506 (tptp) cc_final: 0.6159 (mmmm) REVERT: E 437 GLN cc_start: 0.7827 (tt0) cc_final: 0.7558 (tm-30) REVERT: F 290 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7812 (t70) REVERT: G 74 GLU cc_start: 0.2021 (OUTLIER) cc_final: 0.1654 (pt0) REVERT: G 148 LYS cc_start: 0.6306 (mmmt) cc_final: 0.5937 (tppt) REVERT: G 159 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6995 (ptm160) REVERT: G 196 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6825 (ttm-80) REVERT: G 200 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6572 (mmmt) REVERT: G 201 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6175 (mp) REVERT: H 1 MET cc_start: 0.1455 (mtt) cc_final: -0.0598 (ppp) REVERT: I 104 MET cc_start: 0.1014 (mmp) cc_final: 0.0712 (ptt) REVERT: J 110 GLU cc_start: 0.5410 (tp30) cc_final: 0.4813 (mm-30) REVERT: J 153 ARG cc_start: 0.4490 (OUTLIER) cc_final: 0.4232 (tmm160) REVERT: J 161 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7671 (t) REVERT: J 173 ARG cc_start: 0.5138 (ttm-80) cc_final: 0.3860 (ttp80) REVERT: L 143 GLN cc_start: 0.6154 (mt0) cc_final: 0.5489 (mp10) REVERT: L 168 LEU cc_start: 0.6028 (mt) cc_final: 0.5567 (tt) outliers start: 87 outliers final: 40 residues processed: 289 average time/residue: 0.8490 time to fit residues: 280.5842 Evaluate side-chains 276 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain J residue 161 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 282 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 287 optimal weight: 7.9990 chunk 335 optimal weight: 20.0000 chunk 283 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN F 310 GLN G 180 GLN G 185 GLN J 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.130703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099814 restraints weight = 51530.930| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.02 r_work: 0.3349 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 30074 Z= 0.263 Angle : 0.654 10.676 40754 Z= 0.337 Chirality : 0.048 0.193 4567 Planarity : 0.006 0.060 5336 Dihedral : 5.626 87.134 4230 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.11 % Allowed : 15.44 % Favored : 81.44 % 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: 0.36 (0.14), residues: 3761 helix: 1.36 (0.13), residues: 1536 sheet: -0.41 (0.22), residues: 557 loop : -0.51 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 105 TYR 0.025 0.002 TYR G 133 PHE 0.022 0.002 PHE C 559 TRP 0.017 0.002 TRP B 119 HIS 0.009 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00643 (30074) covalent geometry : angle 0.65429 (40754) hydrogen bonds : bond 0.05515 ( 1326) hydrogen bonds : angle 4.87617 ( 3783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 221 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6544 (mtt) REVERT: A 95 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7414 (tmt90) REVERT: A 109 HIS cc_start: 0.7945 (m-70) cc_final: 0.7728 (m-70) REVERT: A 122 MET cc_start: 0.7876 (mtp) cc_final: 0.7143 (tmm) REVERT: A 180 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6802 (mm-30) REVERT: A 257 GLU cc_start: 0.7413 (tp30) cc_final: 0.6986 (mm-30) REVERT: A 441 GLU cc_start: 0.8499 (tp30) cc_final: 0.8044 (mp0) REVERT: A 481 ARG cc_start: 0.6927 (tpt-90) cc_final: 0.6374 (mtm110) REVERT: A 520 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 531 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6855 (mtmm) REVERT: B 156 ARG cc_start: 0.7445 (ptm-80) cc_final: 0.7160 (ptp-170) REVERT: B 165 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: B 176 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7379 (mt-10) REVERT: B 243 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7854 (ttmt) REVERT: B 340 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7332 (ttm-80) REVERT: B 436 ASP cc_start: 0.6880 (m-30) cc_final: 0.6659 (m-30) REVERT: B 459 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7553 (mm110) REVERT: B 460 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7092 (ttp80) REVERT: B 496 GLN cc_start: 0.8746 (tt0) cc_final: 0.8317 (tp40) REVERT: B 550 ARG cc_start: 0.7215 (tpt90) cc_final: 0.7009 (tpt90) REVERT: C 169 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8028 (mm-30) REVERT: C 170 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: C 336 GLU cc_start: 0.8300 (tp30) cc_final: 0.7847 (tp30) REVERT: C 524 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7626 (tmmt) REVERT: C 546 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6761 (tm-30) REVERT: D 119 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8428 (tt) REVERT: D 185 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5624 (mm-30) REVERT: D 265 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: D 280 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7850 (mtp-110) REVERT: D 287 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8602 (ttt) REVERT: D 420 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7671 (tpp-160) REVERT: E 26 ASP cc_start: 0.8386 (m-30) cc_final: 0.7754 (t0) REVERT: E 88 MET cc_start: 0.8322 (mtp) cc_final: 0.7769 (mtt) REVERT: E 305 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7979 (mptp) REVERT: E 394 LYS cc_start: 0.6433 (tptp) cc_final: 0.6120 (mmmm) REVERT: E 437 GLN cc_start: 0.7840 (tt0) cc_final: 0.7550 (tm-30) REVERT: F 290 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7864 (t70) REVERT: G 74 GLU cc_start: 0.2206 (OUTLIER) cc_final: 0.1771 (pt0) REVERT: G 148 LYS cc_start: 0.6249 (mmmt) cc_final: 0.5882 (tppt) REVERT: G 159 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7013 (ptm160) REVERT: G 196 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6890 (ttm-80) REVERT: G 200 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6316 (tmtt) REVERT: G 201 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6262 (mp) REVERT: H 1 MET cc_start: 0.1116 (mtt) cc_final: 0.0780 (pmm) REVERT: H 84 HIS cc_start: 0.1306 (OUTLIER) cc_final: 0.0652 (t-170) REVERT: I 104 MET cc_start: 0.1101 (mmp) cc_final: 0.0789 (ptt) REVERT: J 110 GLU cc_start: 0.5608 (tp30) cc_final: 0.5000 (mm-30) REVERT: J 153 ARG cc_start: 0.4401 (OUTLIER) cc_final: 0.4097 (tmm160) REVERT: J 161 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7692 (t) REVERT: J 173 ARG cc_start: 0.5183 (ttm-80) cc_final: 0.3890 (ttp80) REVERT: L 143 GLN cc_start: 0.6429 (mt0) cc_final: 0.5726 (mp10) outliers start: 96 outliers final: 44 residues processed: 292 average time/residue: 0.8374 time to fit residues: 279.8723 Evaluate side-chains 285 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 249 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 372 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 155 optimal weight: 0.0470 chunk 296 optimal weight: 0.8980 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN G 180 GLN G 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.133911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103206 restraints weight = 50904.281| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.00 r_work: 0.3428 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30074 Z= 0.111 Angle : 0.524 11.017 40754 Z= 0.267 Chirality : 0.043 0.203 4567 Planarity : 0.005 0.064 5336 Dihedral : 5.093 83.443 4230 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.91 % Allowed : 16.90 % Favored : 81.18 % 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: 0.75 (0.14), residues: 3761 helix: 1.67 (0.14), residues: 1567 sheet: -0.29 (0.22), residues: 550 loop : -0.30 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 154 TYR 0.016 0.001 TYR G 133 PHE 0.011 0.001 PHE G 130 TRP 0.016 0.001 TRP B 119 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00251 (30074) covalent geometry : angle 0.52357 (40754) hydrogen bonds : bond 0.03969 ( 1326) hydrogen bonds : angle 4.52968 ( 3783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6405 (mtt) REVERT: A 95 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7478 (tmt90) REVERT: A 109 HIS cc_start: 0.7896 (m-70) cc_final: 0.7694 (m-70) REVERT: A 122 MET cc_start: 0.7708 (mtp) cc_final: 0.7105 (tmm) REVERT: A 180 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6725 (mm-30) REVERT: A 257 GLU cc_start: 0.7332 (tp30) cc_final: 0.6913 (mm-30) REVERT: A 441 GLU cc_start: 0.8425 (tp30) cc_final: 0.8100 (mp0) REVERT: A 481 ARG cc_start: 0.6889 (tpt-90) cc_final: 0.6385 (mtm110) REVERT: A 520 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 154 ARG cc_start: 0.7783 (ptm160) cc_final: 0.7199 (ptm-80) REVERT: B 156 ARG cc_start: 0.7189 (ptm-80) cc_final: 0.6835 (ptp-170) REVERT: B 165 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: B 176 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7269 (mt-10) REVERT: B 264 ASP cc_start: 0.8298 (m-30) cc_final: 0.8086 (m-30) REVERT: B 340 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7017 (ttm-80) REVERT: B 436 ASP cc_start: 0.6830 (m-30) cc_final: 0.6629 (m-30) REVERT: B 459 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7556 (mm110) REVERT: B 496 GLN cc_start: 0.8692 (tt0) cc_final: 0.8255 (tp40) REVERT: B 550 ARG cc_start: 0.7055 (tpt90) cc_final: 0.6782 (tpt90) REVERT: C 133 MET cc_start: 0.8354 (mtp) cc_final: 0.8118 (mtp) REVERT: C 169 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7949 (mm-30) REVERT: C 336 GLU cc_start: 0.8335 (tp30) cc_final: 0.7890 (tp30) REVERT: C 478 ASP cc_start: 0.6310 (m-30) cc_final: 0.5861 (m-30) REVERT: C 524 LYS cc_start: 0.7999 (mmpt) cc_final: 0.7569 (tmmt) REVERT: C 546 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6662 (tm-30) REVERT: D 265 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: D 280 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7807 (mtp-110) REVERT: D 287 MET cc_start: 0.8930 (ttt) cc_final: 0.8644 (ttt) REVERT: D 420 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7588 (tpp-160) REVERT: E 26 ASP cc_start: 0.8260 (m-30) cc_final: 0.7772 (t0) REVERT: E 394 LYS cc_start: 0.6427 (tptp) cc_final: 0.6101 (mmmm) REVERT: E 437 GLN cc_start: 0.7757 (tt0) cc_final: 0.7507 (tm-30) REVERT: G 159 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6972 (ptm160) REVERT: G 196 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6839 (ttm-80) REVERT: H 1 MET cc_start: 0.2124 (mtt) cc_final: 0.0839 (pmm) REVERT: J 110 GLU cc_start: 0.5223 (tp30) cc_final: 0.4695 (mm-30) REVERT: J 161 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7668 (t) REVERT: J 173 ARG cc_start: 0.5037 (ttm-80) cc_final: 0.3814 (ttp80) REVERT: L 142 LEU cc_start: 0.6544 (pt) cc_final: 0.6204 (pt) REVERT: L 143 GLN cc_start: 0.6389 (mt0) cc_final: 0.5707 (mp10) REVERT: L 168 LEU cc_start: 0.6115 (mt) cc_final: 0.5563 (tt) outliers start: 59 outliers final: 29 residues processed: 281 average time/residue: 0.8439 time to fit residues: 270.8164 Evaluate side-chains 257 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain J residue 161 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 337 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 295 optimal weight: 0.0670 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN F 166 GLN F 170 GLN G 180 GLN G 185 GLN H 84 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.132065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101486 restraints weight = 51033.806| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.99 r_work: 0.3402 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30074 Z= 0.183 Angle : 0.590 10.916 40754 Z= 0.301 Chirality : 0.045 0.191 4567 Planarity : 0.005 0.064 5336 Dihedral : 5.243 84.334 4230 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.72 % Allowed : 17.46 % Favored : 80.82 % 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: 0.64 (0.14), residues: 3761 helix: 1.57 (0.13), residues: 1569 sheet: -0.31 (0.22), residues: 557 loop : -0.36 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 154 TYR 0.019 0.001 TYR G 133 PHE 0.018 0.002 PHE C 559 TRP 0.014 0.002 TRP B 119 HIS 0.007 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00444 (30074) covalent geometry : angle 0.59046 (40754) hydrogen bonds : bond 0.04650 ( 1326) hydrogen bonds : angle 4.64158 ( 3783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7474 (tmt90) REVERT: A 122 MET cc_start: 0.7747 (mtp) cc_final: 0.7083 (tmm) REVERT: A 180 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6727 (mm-30) REVERT: A 257 GLU cc_start: 0.7392 (tp30) cc_final: 0.6959 (mm-30) REVERT: A 441 GLU cc_start: 0.8419 (tp30) cc_final: 0.8111 (mp0) REVERT: A 481 ARG cc_start: 0.6938 (tpt-90) cc_final: 0.6431 (mtm110) REVERT: A 520 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 156 ARG cc_start: 0.7275 (ptm-80) cc_final: 0.6921 (ptp-170) REVERT: B 165 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: B 176 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7316 (mt-10) REVERT: B 340 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7196 (ttm-80) REVERT: B 459 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7574 (mm110) REVERT: B 496 GLN cc_start: 0.8728 (tt0) cc_final: 0.8304 (tp40) REVERT: B 550 ARG cc_start: 0.7142 (tpt90) cc_final: 0.6851 (tpt90) REVERT: C 169 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8007 (mm-30) REVERT: C 336 GLU cc_start: 0.8319 (tp30) cc_final: 0.7871 (tp30) REVERT: C 478 ASP cc_start: 0.6560 (m-30) cc_final: 0.6094 (m-30) REVERT: C 524 LYS cc_start: 0.8044 (mmpt) cc_final: 0.7616 (tmmt) REVERT: C 546 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6676 (tm-30) REVERT: D 265 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: D 280 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7870 (mtp-110) REVERT: D 420 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7640 (tpp-160) REVERT: E 26 ASP cc_start: 0.8292 (m-30) cc_final: 0.7801 (t0) REVERT: E 362 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7641 (tpp) REVERT: E 394 LYS cc_start: 0.6407 (tptp) cc_final: 0.6055 (mmmm) REVERT: E 437 GLN cc_start: 0.7783 (tt0) cc_final: 0.7555 (tm-30) REVERT: G 148 LYS cc_start: 0.6351 (mmmt) cc_final: 0.5958 (tppt) REVERT: G 159 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6948 (ptm160) REVERT: G 196 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6971 (ttm-80) REVERT: H 1 MET cc_start: 0.2002 (mtt) cc_final: -0.0421 (ppp) REVERT: J 110 GLU cc_start: 0.5222 (tp30) cc_final: 0.4763 (mm-30) REVERT: J 161 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7638 (t) REVERT: J 173 ARG cc_start: 0.5203 (ttm-80) cc_final: 0.3896 (ttp80) REVERT: L 142 LEU cc_start: 0.6530 (pt) cc_final: 0.6303 (pt) REVERT: L 143 GLN cc_start: 0.6634 (mt0) cc_final: 0.5955 (mp10) REVERT: L 168 LEU cc_start: 0.6079 (mt) cc_final: 0.5581 (tt) outliers start: 53 outliers final: 32 residues processed: 255 average time/residue: 0.8310 time to fit residues: 242.4558 Evaluate side-chains 253 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 196 ARG Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain J residue 161 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 317 optimal weight: 0.7980 chunk 161 optimal weight: 0.3980 chunk 95 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN G 180 GLN G 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.132438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.101967 restraints weight = 51332.556| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.00 r_work: 0.3408 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30074 Z= 0.152 Angle : 0.558 10.783 40754 Z= 0.285 Chirality : 0.044 0.193 4567 Planarity : 0.005 0.064 5336 Dihedral : 5.178 84.295 4230 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.91 % Allowed : 17.49 % Favored : 80.60 % 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: 3761 helix: 1.59 (0.13), residues: 1569 sheet: -0.32 (0.22), residues: 547 loop : -0.36 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 154 TYR 0.019 0.001 TYR G 133 PHE 0.014 0.001 PHE C 559 TRP 0.014 0.001 TRP B 119 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00364 (30074) covalent geometry : angle 0.55850 (40754) hydrogen bonds : bond 0.04386 ( 1326) hydrogen bonds : angle 4.61093 ( 3783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12680.92 seconds wall clock time: 215 minutes 39.52 seconds (12939.52 seconds total)