Starting phenix.real_space_refine on Sun Jul 5 17:52:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7var_31860/07_2026/7var_31860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7var_31860/07_2026/7var_31860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7var_31860/07_2026/7var_31860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7var_31860/07_2026/7var_31860.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7var_31860/07_2026/7var_31860.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7var_31860/07_2026/7var_31860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7var_31860/07_2026/7var_31860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7var_31860/07_2026/7var_31860.map" } resolution = 2.9 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 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.95, per 1000 atoms: 0.20 Number of scatterers: 29520 At special positions: 0 Unit cell: (140.8, 174.24, 150.48, 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: 2.16 Conformation dependent library (CDL) restraints added in 1.2 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 24 sheets defined 47.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 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: 4.154A 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: 4.408A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.109A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 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: 3.970A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.605A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for '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: 3.524A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.865A 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: 3.678A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 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: 4.738A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.666A 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 removed outlier: 3.555A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.604A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (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 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: 3.784A 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 576 removed outlier: 3.565A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.833A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.214A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.146A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.523A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.164A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.567A pdb=" N GLN C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.863A 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: 3.749A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 4.152A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.502A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.517A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.111A 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: 3.662A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.595A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.564A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.252A 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: 3.911A 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: 3.978A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 removed outlier: 3.616A pdb=" N MET E 141 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.059A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.859A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.880A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.592A 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 Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.193A 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 447 through 451 removed outlier: 3.575A pdb=" N LEU E 451 " --> pdb=" O GLN E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.552A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.830A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.734A 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 removed outlier: 3.512A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 374 through 399 removed outlier: 3.527A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) 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 471 removed outlier: 3.886A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.913A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.594A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 removed outlier: 3.794A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.582A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 208 removed outlier: 3.605A 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 59 Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 85 through 99 removed outlier: 3.729A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 105 removed outlier: 4.507A pdb=" N ARG I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.548A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 removed outlier: 3.712A 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: 3.573A 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 139 Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.523A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.639A 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: 3.877A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 removed outlier: 3.646A pdb=" N GLU K 117 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 127 through 130 Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.513A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 188 removed outlier: 4.578A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.608A 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: 6.509A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.140A 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: 5.753A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.589A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.798A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 6.544A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.818A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.643A 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: 5.677A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 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: 3.928A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (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 117 through 119 removed outlier: 3.624A 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: 7.011A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.520A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 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=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 148 removed outlier: 6.415A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.761A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.621A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 93 current: chain 'D' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 223 current: chain 'D' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 307 through 315 current: chain 'D' and resid 358 through 359 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.662A 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 94 Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.736A 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: 3.688A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 94 current: chain 'F' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 223 current: chain 'F' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 307 through 315 current: chain 'F' and resid 358 through 359 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.705A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC6, first strand: chain 'H' and resid 19 through 22 removed outlier: 8.114A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3618 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: 5.17 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9966 1.34 - 1.46: 5196 1.46 - 1.58: 14709 1.58 - 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 1.385 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.590 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" N ARG F 372 " pdb=" CA ARG F 372 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.87e+00 bond pdb=" N GLU D 296 " pdb=" CA GLU D 296 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.14e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 40645 3.24 - 6.49: 99 6.49 - 9.73: 8 9.73 - 12.98: 1 12.98 - 16.22: 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 120.50 136.72 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O2B ADP A 601 " ideal model delta sigma weight residual 119.90 106.99 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N THR G 119 " pdb=" CA THR G 119 " pdb=" C THR G 119 " ideal model delta sigma weight residual 109.81 117.95 -8.14 2.21e+00 2.05e-01 1.36e+01 angle pdb=" CA ALA D 298 " pdb=" C ALA D 298 " pdb=" O ALA D 298 " ideal model delta sigma weight residual 121.56 117.98 3.58 1.09e+00 8.42e-01 1.08e+01 angle pdb=" C ALA E 441 " pdb=" N LEU E 442 " pdb=" CA LEU E 442 " ideal model delta sigma weight residual 122.06 116.03 6.03 1.86e+00 2.89e-01 1.05e+01 ... (remaining 40749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 17738 27.89 - 55.78: 497 55.78 - 83.67: 71 83.67 - 111.56: 10 111.56 - 139.45: 2 Dihedral angle restraints: 18318 sinusoidal: 7500 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 79.45 -139.45 1 2.00e+01 2.50e-03 4.22e+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 78.40 -138.41 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" C THR F 371 " pdb=" N THR F 371 " pdb=" CA THR F 371 " pdb=" CB THR F 371 " ideal model delta harmonic sigma weight residual -122.00 -137.73 15.73 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 18315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4331 0.095 - 0.191: 235 0.191 - 0.286: 0 0.286 - 0.381: 0 0.381 - 0.477: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA THR F 371 " pdb=" N THR F 371 " pdb=" C THR F 371 " pdb=" CB THR F 371 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 4564 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 124 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO L 125 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO L 125 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 125 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 101 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO G 102 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 102 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 102 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO E 324 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 168 2.61 - 3.18: 25085 3.18 - 3.76: 44702 3.76 - 4.33: 63216 4.33 - 4.90: 106582 Nonbonded interactions: 239753 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 2.038 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.065 2.170 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLU H 28 " model vdw 2.145 3.040 nonbonded pdb=" OD1 ASP F 34 " pdb=" OG SER F 74 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.228 3.040 ... (remaining 239748 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 24.210 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.003 0.105 30074 Z= 0.143 Angle : 0.556 16.222 40754 Z= 0.308 Chirality : 0.043 0.477 4567 Planarity : 0.004 0.059 5336 Dihedral : 13.207 139.447 11402 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.06 % Allowed : 0.26 % Favored : 99.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.14), residues: 3761 helix: 1.89 (0.14), residues: 1554 sheet: 0.35 (0.22), residues: 579 loop : 0.42 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 364 TYR 0.010 0.001 TYR G 133 PHE 0.009 0.001 PHE B 143 TRP 0.006 0.001 TRP C 119 HIS 0.003 0.001 HIS F 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (30074) covalent geometry : angle 0.55562 / 0.31 (40754) hydrogen bonds : bond 0.15593 / 10.88 ( 1269) hydrogen bonds : angle 5.84262 / 4.10 ( 3618) *********************** 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 509 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 507 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8104 (ptpp) cc_final: 0.7625 (mttp) REVERT: A 143 PHE cc_start: 0.8529 (m-80) cc_final: 0.8188 (m-10) REVERT: A 154 ARG cc_start: 0.7613 (ptm160) cc_final: 0.7105 (ptt90) REVERT: A 445 GLU cc_start: 0.7852 (tp30) cc_final: 0.7442 (tp30) REVERT: A 502 GLU cc_start: 0.7829 (pm20) cc_final: 0.7395 (mp0) REVERT: A 524 LYS cc_start: 0.7697 (mmtp) cc_final: 0.7412 (ptmt) REVERT: A 546 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6668 (mm-30) REVERT: A 547 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.7127 (ttm110) REVERT: B 38 GLU cc_start: 0.7968 (tt0) cc_final: 0.7610 (tt0) REVERT: B 130 ARG cc_start: 0.7341 (mmt-90) cc_final: 0.7077 (mpt180) REVERT: B 467 ILE cc_start: 0.6882 (mm) cc_final: 0.6523 (mt) REVERT: B 502 GLU cc_start: 0.8006 (tt0) cc_final: 0.7764 (mp0) REVERT: C 121 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8775 (Cg_exo) REVERT: C 140 GLU cc_start: 0.7594 (tp30) cc_final: 0.7215 (tt0) REVERT: C 488 ARG cc_start: 0.7943 (tmm-80) cc_final: 0.7577 (ttp-170) REVERT: C 546 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7397 (pt0) REVERT: C 550 ARG cc_start: 0.7615 (ttp-110) cc_final: 0.6888 (ttm-80) REVERT: D 74 SER cc_start: 0.8315 (t) cc_final: 0.8100 (m) REVERT: D 275 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7718 (mt-10) REVERT: D 453 ARG cc_start: 0.7418 (mtp85) cc_final: 0.7153 (mtp85) REVERT: E 196 ILE cc_start: 0.8083 (mm) cc_final: 0.7393 (pt) REVERT: E 206 GLN cc_start: 0.7360 (mt0) cc_final: 0.7136 (mp10) REVERT: E 274 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7207 (mtm-85) REVERT: E 410 ARG cc_start: 0.6981 (ttm110) cc_final: 0.6770 (ttt90) REVERT: F 98 LYS cc_start: 0.7501 (mmtm) cc_final: 0.7214 (mmpt) REVERT: F 128 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7376 (mm-30) REVERT: F 178 SER cc_start: 0.8043 (t) cc_final: 0.7735 (p) REVERT: F 210 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7704 (ttm170) REVERT: G 30 LYS cc_start: 0.7502 (mtpp) cc_final: 0.7260 (mttt) REVERT: G 38 GLU cc_start: 0.6987 (tt0) cc_final: 0.6361 (tp30) REVERT: G 96 VAL cc_start: 0.7218 (t) cc_final: 0.6973 (m) REVERT: G 149 LYS cc_start: 0.7259 (mmtt) cc_final: 0.6709 (mtmt) REVERT: H 19 GLU cc_start: 0.4165 (tt0) cc_final: 0.3625 (tp30) REVERT: H 28 GLU cc_start: 0.4253 (pm20) cc_final: 0.3946 (tt0) REVERT: J 122 VAL cc_start: 0.6143 (t) cc_final: 0.5764 (p) REVERT: J 134 LEU cc_start: 0.4500 (pt) cc_final: 0.3618 (mp) REVERT: K 91 ARG cc_start: 0.4595 (ttm170) cc_final: 0.4266 (mtp85) REVERT: K 104 MET cc_start: 0.5725 (ttm) cc_final: 0.5203 (ttp) REVERT: L 105 ARG cc_start: 0.6833 (mtm-85) cc_final: 0.6497 (mtm-85) REVERT: L 119 LYS cc_start: 0.7084 (pttt) cc_final: 0.6746 (pttp) REVERT: L 172 ASP cc_start: 0.7519 (m-30) cc_final: 0.7155 (t0) REVERT: L 181 LYS cc_start: 0.6696 (mmmt) cc_final: 0.6395 (mttm) REVERT: L 187 TRP cc_start: 0.6663 (m-90) cc_final: 0.6377 (m-90) outliers start: 2 outliers final: 1 residues processed: 509 average time/residue: 0.8712 time to fit residues: 500.6890 Evaluate side-chains 293 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 363 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN A 571 GLN B 202 ASN B 260 ASN B 423 ASN C 238 GLN D 364 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 181 GLN L 165 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089355 restraints weight = 44694.033| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.68 r_work: 0.2982 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30074 Z= 0.130 Angle : 0.525 7.790 40754 Z= 0.269 Chirality : 0.044 0.164 4567 Planarity : 0.005 0.050 5336 Dihedral : 5.426 139.032 4201 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.52 % Allowed : 8.34 % Favored : 90.14 % 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: 1.50 (0.14), residues: 3761 helix: 1.92 (0.14), residues: 1564 sheet: 0.48 (0.22), residues: 555 loop : 0.39 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 210 TYR 0.013 0.001 TYR G 133 PHE 0.012 0.001 PHE C 230 TRP 0.014 0.001 TRP A 119 HIS 0.011 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (30074) covalent geometry : angle 0.52532 / 0.27 (40754) hydrogen bonds : bond 0.04834 / 3.28 ( 1269) hydrogen bonds : angle 4.63663 / 3.24 ( 3618) *********************** 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 362 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8226 (mmm) cc_final: 0.7646 (mmm) REVERT: A 124 LYS cc_start: 0.8269 (ptpp) cc_final: 0.7726 (mttp) REVERT: A 154 ARG cc_start: 0.7847 (ptm160) cc_final: 0.7372 (ptt90) REVERT: A 323 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8045 (mtt) REVERT: A 502 GLU cc_start: 0.8149 (pm20) cc_final: 0.7730 (mp0) REVERT: A 547 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7331 (ttm110) REVERT: B 38 GLU cc_start: 0.8613 (tt0) cc_final: 0.8412 (tt0) REVERT: B 130 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7620 (mpt180) REVERT: B 170 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7409 (tp30) REVERT: B 408 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8435 (ttt-90) REVERT: B 467 ILE cc_start: 0.7204 (mm) cc_final: 0.6937 (mt) REVERT: B 502 GLU cc_start: 0.8577 (tt0) cc_final: 0.8088 (mp0) REVERT: B 513 TYR cc_start: 0.8094 (t80) cc_final: 0.7588 (t80) REVERT: B 571 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6437 (mp10) REVERT: C 294 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8191 (mtp) REVERT: C 323 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7995 (mmt) REVERT: C 441 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: C 488 ARG cc_start: 0.8749 (tmm-80) cc_final: 0.8387 (ttp-170) REVERT: C 550 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7640 (ttm-80) REVERT: D 25 LYS cc_start: 0.8417 (ptpt) cc_final: 0.8098 (mtpt) REVERT: D 416 ASP cc_start: 0.8486 (m-30) cc_final: 0.8155 (m-30) REVERT: E 162 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: E 410 ARG cc_start: 0.7286 (ttm110) cc_final: 0.7009 (ttt90) REVERT: F 128 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8235 (mm-30) REVERT: F 210 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8235 (ttm170) REVERT: F 391 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: G 38 GLU cc_start: 0.7816 (tt0) cc_final: 0.7130 (tp30) REVERT: G 137 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7132 (mt) REVERT: G 149 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7380 (mppt) REVERT: H 28 GLU cc_start: 0.5070 (pm20) cc_final: 0.4528 (tt0) REVERT: J 134 LEU cc_start: 0.4357 (pt) cc_final: 0.3781 (mp) REVERT: J 148 LEU cc_start: 0.3032 (tp) cc_final: 0.2519 (pp) REVERT: J 172 ASP cc_start: 0.5642 (m-30) cc_final: 0.5414 (m-30) REVERT: K 91 ARG cc_start: 0.4751 (ttm170) cc_final: 0.4416 (mtp85) REVERT: K 104 MET cc_start: 0.5740 (ttm) cc_final: 0.5504 (ttp) REVERT: L 119 LYS cc_start: 0.7360 (pttt) cc_final: 0.7086 (pttp) REVERT: L 165 ASN cc_start: 0.7556 (t0) cc_final: 0.7191 (t160) REVERT: L 181 LYS cc_start: 0.7124 (mmmt) cc_final: 0.6754 (mttm) outliers start: 47 outliers final: 9 residues processed: 347 average time/residue: 0.9050 time to fit residues: 355.1292 Evaluate side-chains 289 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 220 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS A 316 GLN A 541 GLN A 571 GLN E 58 GLN F 310 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.085678 restraints weight = 44890.584| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.71 r_work: 0.2917 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30074 Z= 0.255 Angle : 0.644 10.319 40754 Z= 0.331 Chirality : 0.049 0.185 4567 Planarity : 0.006 0.056 5336 Dihedral : 5.982 154.523 4199 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.73 % Allowed : 10.67 % Favored : 86.60 % 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: 0.91 (0.14), residues: 3761 helix: 1.49 (0.13), residues: 1548 sheet: 0.06 (0.21), residues: 579 loop : 0.06 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 453 TYR 0.017 0.002 TYR B 304 PHE 0.015 0.002 PHE D 191 TRP 0.018 0.002 TRP G 97 HIS 0.008 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.25 (30074) covalent geometry : angle 0.64368 / 0.33 (40754) hydrogen bonds : bond 0.06221 / 4.20 ( 1269) hydrogen bonds : angle 4.75085 / 3.33 ( 3618) *********************** 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 360 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 276 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8387 (ptpp) cc_final: 0.7745 (mttp) REVERT: A 154 ARG cc_start: 0.7874 (ptm160) cc_final: 0.7358 (ptt90) REVERT: A 323 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8068 (mtt) REVERT: A 502 GLU cc_start: 0.8075 (pm20) cc_final: 0.7729 (mp0) REVERT: A 547 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7486 (ttt90) REVERT: A 550 ARG cc_start: 0.8191 (mmt90) cc_final: 0.7195 (mtp-110) REVERT: B 93 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7554 (mpp80) REVERT: B 170 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7409 (tp30) REVERT: B 314 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.7937 (ptt90) REVERT: B 408 ARG cc_start: 0.8664 (ttm-80) cc_final: 0.8411 (ttt-90) REVERT: B 410 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: B 450 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8448 (tp) REVERT: B 467 ILE cc_start: 0.7111 (mm) cc_final: 0.6827 (mt) REVERT: B 502 GLU cc_start: 0.8535 (tt0) cc_final: 0.8122 (mp0) REVERT: B 567 MET cc_start: 0.7820 (tpt) cc_final: 0.7468 (tpt) REVERT: C 124 LYS cc_start: 0.8285 (mppt) cc_final: 0.7608 (mmmt) REVERT: C 323 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7918 (mmt) REVERT: C 441 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: C 532 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.5815 (mtp85) REVERT: C 550 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7651 (ttm-80) REVERT: D 25 LYS cc_start: 0.8414 (ptpt) cc_final: 0.7950 (mtpt) REVERT: D 206 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: D 413 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: E 162 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: E 410 ARG cc_start: 0.7471 (ttm110) cc_final: 0.7181 (ttt90) REVERT: E 452 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7520 (mtpt) REVERT: F 275 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8684 (mt-10) REVERT: F 373 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8176 (pt0) REVERT: F 391 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8131 (m-30) REVERT: G 13 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8390 (tp40) REVERT: G 38 GLU cc_start: 0.7908 (tt0) cc_final: 0.7248 (tp30) REVERT: G 137 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7143 (mt) REVERT: G 139 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6786 (ttm-80) REVERT: G 148 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7291 (mttp) REVERT: G 149 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7399 (mtmt) REVERT: H 77 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5835 (tm) REVERT: H 91 ARG cc_start: 0.6564 (mmm160) cc_final: 0.5816 (mmp80) REVERT: J 148 LEU cc_start: 0.2868 (tp) cc_final: 0.2533 (pp) REVERT: J 164 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5369 (tp30) REVERT: J 172 ASP cc_start: 0.5662 (m-30) cc_final: 0.5393 (m-30) REVERT: K 91 ARG cc_start: 0.4533 (ttm170) cc_final: 0.4201 (mtp85) REVERT: K 104 MET cc_start: 0.5605 (ttm) cc_final: 0.5290 (ttp) REVERT: L 119 LYS cc_start: 0.7421 (pttt) cc_final: 0.7116 (pttp) outliers start: 84 outliers final: 25 residues processed: 341 average time/residue: 0.8233 time to fit residues: 320.3086 Evaluate side-chains 307 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 330 optimal weight: 0.9980 chunk 326 optimal weight: 8.9990 chunk 284 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 0.0170 chunk 364 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 368 optimal weight: 20.0000 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN A 571 GLN L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089062 restraints weight = 44383.293| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.85 r_work: 0.2960 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30074 Z= 0.112 Angle : 0.502 10.208 40754 Z= 0.256 Chirality : 0.043 0.190 4567 Planarity : 0.005 0.044 5336 Dihedral : 5.540 159.971 4199 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.85 % Allowed : 12.36 % Favored : 85.79 % 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: 1.22 (0.14), residues: 3761 helix: 1.86 (0.14), residues: 1545 sheet: 0.16 (0.21), residues: 580 loop : 0.13 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 130 TYR 0.013 0.001 TYR G 133 PHE 0.014 0.001 PHE A 230 TRP 0.016 0.001 TRP G 97 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (30074) covalent geometry : angle 0.50170 / 0.26 (40754) hydrogen bonds : bond 0.04436 / 3.01 ( 1269) hydrogen bonds : angle 4.40587 / 3.08 ( 3618) *********************** 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 331 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8330 (ptpp) cc_final: 0.7733 (mttp) REVERT: A 143 PHE cc_start: 0.8830 (m-80) cc_final: 0.8547 (m-10) REVERT: A 154 ARG cc_start: 0.7908 (ptm160) cc_final: 0.7354 (ptt90) REVERT: A 323 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8006 (mtt) REVERT: A 502 GLU cc_start: 0.8140 (pm20) cc_final: 0.7785 (mp0) REVERT: A 524 LYS cc_start: 0.8547 (ptmt) cc_final: 0.7946 (mttt) REVERT: A 547 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7442 (ttt90) REVERT: B 156 ARG cc_start: 0.8156 (ptm160) cc_final: 0.7936 (tmm-80) REVERT: B 170 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: B 314 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7892 (ptt90) REVERT: B 408 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8401 (ttt-90) REVERT: B 467 ILE cc_start: 0.7057 (mm) cc_final: 0.6791 (mt) REVERT: B 502 GLU cc_start: 0.8608 (tt0) cc_final: 0.8115 (mp0) REVERT: B 513 TYR cc_start: 0.8109 (t80) cc_final: 0.7594 (t80) REVERT: B 557 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: B 571 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: C 124 LYS cc_start: 0.8209 (mppt) cc_final: 0.7541 (mmmt) REVERT: C 133 MET cc_start: 0.8520 (mtm) cc_final: 0.8306 (mtt) REVERT: C 323 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.7996 (mmt) REVERT: C 441 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: C 532 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.5651 (mtp85) REVERT: C 550 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7569 (ttm-80) REVERT: D 413 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: D 416 ASP cc_start: 0.8447 (m-30) cc_final: 0.8139 (m-30) REVERT: E 410 ARG cc_start: 0.7435 (ttm110) cc_final: 0.7095 (ttt90) REVERT: F 128 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8229 (mm-30) REVERT: F 210 ARG cc_start: 0.8350 (ttm170) cc_final: 0.8097 (ttm170) REVERT: F 391 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: G 13 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8237 (tp40) REVERT: G 38 GLU cc_start: 0.7793 (tt0) cc_final: 0.7113 (tp30) REVERT: G 148 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7223 (mttp) REVERT: G 149 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7517 (mppt) REVERT: H 77 LEU cc_start: 0.6381 (tp) cc_final: 0.6051 (tp) REVERT: H 91 ARG cc_start: 0.6560 (mmm160) cc_final: 0.5833 (mmp80) REVERT: J 148 LEU cc_start: 0.2772 (tp) cc_final: 0.2518 (pp) REVERT: J 172 ASP cc_start: 0.5743 (m-30) cc_final: 0.5419 (OUTLIER) REVERT: K 91 ARG cc_start: 0.4620 (ttm170) cc_final: 0.4257 (mtp85) REVERT: K 117 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6446 (mt-10) outliers start: 57 outliers final: 14 residues processed: 318 average time/residue: 0.8315 time to fit residues: 300.8316 Evaluate side-chains 273 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 100 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 325 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 286 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN A 571 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 = 0.3538 r_free = 0.3538 target = 0.119685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.086744 restraints weight = 44803.692| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.68 r_work: 0.2937 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30074 Z= 0.197 Angle : 0.570 10.377 40754 Z= 0.292 Chirality : 0.046 0.168 4567 Planarity : 0.005 0.061 5336 Dihedral : 5.807 174.227 4199 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.43 % Allowed : 13.17 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3761 helix: 1.67 (0.14), residues: 1550 sheet: 0.07 (0.21), residues: 587 loop : 0.01 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 130 TYR 0.014 0.001 TYR C 428 PHE 0.014 0.002 PHE C 559 TRP 0.014 0.001 TRP A 119 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (30074) covalent geometry : angle 0.57024 / 0.29 (40754) hydrogen bonds : bond 0.05303 / 3.58 ( 1269) hydrogen bonds : angle 4.50168 / 3.15 ( 3618) *********************** 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 349 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 274 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8346 (ptpp) cc_final: 0.7746 (mttp) REVERT: A 143 PHE cc_start: 0.8861 (m-80) cc_final: 0.8610 (m-10) REVERT: A 154 ARG cc_start: 0.7881 (ptm160) cc_final: 0.7321 (ptt90) REVERT: A 323 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8000 (mtt) REVERT: A 374 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: A 416 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8086 (ttm-80) REVERT: A 502 GLU cc_start: 0.8064 (pm20) cc_final: 0.7729 (mp0) REVERT: A 547 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7452 (ttt90) REVERT: A 550 ARG cc_start: 0.8172 (mmt90) cc_final: 0.7221 (mtp-110) REVERT: B 93 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7438 (mpp80) REVERT: B 170 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: B 314 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7922 (ptt90) REVERT: B 408 ARG cc_start: 0.8671 (ttm-80) cc_final: 0.8442 (ttt-90) REVERT: B 410 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: B 467 ILE cc_start: 0.7060 (mm) cc_final: 0.6766 (mt) REVERT: B 502 GLU cc_start: 0.8573 (tt0) cc_final: 0.8133 (mp0) REVERT: B 567 MET cc_start: 0.7812 (tpt) cc_final: 0.7498 (tpt) REVERT: C 1 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6632 (mmt) REVERT: C 124 LYS cc_start: 0.8303 (mppt) cc_final: 0.7659 (mmmt) REVERT: C 323 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7948 (mmt) REVERT: C 441 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: C 480 GLU cc_start: 0.6888 (pt0) cc_final: 0.6595 (pm20) REVERT: C 532 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5659 (mtp85) REVERT: C 550 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.7635 (ttm-80) REVERT: D 206 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: D 413 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: E 410 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7151 (ttt90) REVERT: E 442 LEU cc_start: 0.8577 (pt) cc_final: 0.8282 (mp) REVERT: E 470 ILE cc_start: 0.5298 (OUTLIER) cc_final: 0.5014 (mp) REVERT: F 373 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8166 (pt0) REVERT: G 13 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8299 (tp40) REVERT: G 38 GLU cc_start: 0.7773 (tt0) cc_final: 0.7115 (tp30) REVERT: G 137 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7096 (mt) REVERT: G 148 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7294 (mttp) REVERT: G 149 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7514 (mppt) REVERT: H 77 LEU cc_start: 0.6286 (tp) cc_final: 0.6053 (tp) REVERT: H 91 ARG cc_start: 0.6534 (mmm160) cc_final: 0.5857 (mmp80) REVERT: J 105 ARG cc_start: 0.5005 (mtt90) cc_final: 0.4726 (ttm110) REVERT: J 148 LEU cc_start: 0.2890 (tp) cc_final: 0.2501 (pp) REVERT: J 164 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5504 (tp30) REVERT: K 91 ARG cc_start: 0.4584 (ttm170) cc_final: 0.4273 (mtp85) REVERT: K 117 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6525 (mt-10) outliers start: 75 outliers final: 30 residues processed: 333 average time/residue: 0.7883 time to fit residues: 300.8472 Evaluate side-chains 304 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 410 ARG Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 338 optimal weight: 30.0000 chunk 182 optimal weight: 0.3980 chunk 238 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 371 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.084725 restraints weight = 44760.078| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.70 r_work: 0.2899 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 30074 Z= 0.320 Angle : 0.686 9.178 40754 Z= 0.354 Chirality : 0.051 0.189 4567 Planarity : 0.006 0.069 5336 Dihedral : 6.190 174.412 4199 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.11 % Allowed : 13.63 % Favored : 83.26 % 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: 1.22 (0.13), residues: 1538 sheet: -0.13 (0.21), residues: 578 loop : -0.27 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 130 TYR 0.017 0.002 TYR C 428 PHE 0.019 0.002 PHE F 130 TRP 0.016 0.002 TRP G 97 HIS 0.007 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.32 (30074) covalent geometry : angle 0.68590 / 0.35 (40754) hydrogen bonds : bond 0.06513 / 4.40 ( 1269) hydrogen bonds : angle 4.78223 / 3.36 ( 3618) *********************** 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 358 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 262 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8370 (ptpp) cc_final: 0.7820 (mttp) REVERT: A 154 ARG cc_start: 0.7869 (ptm160) cc_final: 0.7282 (ptt90) REVERT: A 323 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8100 (mtt) REVERT: A 374 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: A 416 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8106 (ttm-80) REVERT: A 502 GLU cc_start: 0.8042 (pm20) cc_final: 0.7718 (mp0) REVERT: A 547 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7475 (ttt90) REVERT: A 550 ARG cc_start: 0.8280 (mmt90) cc_final: 0.7268 (mtp-110) REVERT: B 93 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7425 (mpp80) REVERT: B 133 MET cc_start: 0.8527 (mtt) cc_final: 0.8272 (mtp) REVERT: B 170 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: B 314 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7917 (ptt90) REVERT: B 408 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8408 (ttt-90) REVERT: B 450 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8449 (tp) REVERT: B 467 ILE cc_start: 0.7222 (mm) cc_final: 0.6851 (mt) REVERT: B 502 GLU cc_start: 0.8615 (tt0) cc_final: 0.8188 (mp0) REVERT: B 567 MET cc_start: 0.7945 (tpt) cc_final: 0.7624 (tpt) REVERT: C 124 LYS cc_start: 0.8360 (mppt) cc_final: 0.7686 (mmmt) REVERT: C 128 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: C 323 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.7941 (mmt) REVERT: C 441 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: C 532 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5903 (mtp85) REVERT: C 550 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.7785 (ttm-80) REVERT: D 206 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: D 413 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8479 (mp10) REVERT: E 162 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: E 334 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: E 410 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7239 (ttt90) REVERT: E 470 ILE cc_start: 0.5317 (OUTLIER) cc_final: 0.5067 (mp) REVERT: F 373 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: G 137 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7055 (mt) REVERT: G 139 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6799 (ttm-80) REVERT: G 148 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7334 (mttp) REVERT: G 149 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7507 (mppt) REVERT: H 77 LEU cc_start: 0.6272 (tp) cc_final: 0.6068 (tp) REVERT: H 91 ARG cc_start: 0.6607 (mmm160) cc_final: 0.5924 (mmp80) REVERT: J 105 ARG cc_start: 0.4955 (mtt90) cc_final: 0.4662 (ttm110) REVERT: J 164 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5896 (mm-30) REVERT: J 172 ASP cc_start: 0.5721 (m-30) cc_final: 0.5349 (OUTLIER) REVERT: K 91 ARG cc_start: 0.4495 (ttm170) cc_final: 0.4144 (mtp85) REVERT: L 184 GLN cc_start: 0.6100 (tt0) cc_final: 0.5811 (tm130) outliers start: 96 outliers final: 42 residues processed: 336 average time/residue: 0.8403 time to fit residues: 323.9395 Evaluate side-chains 315 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 410 ARG Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 75 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 284 optimal weight: 0.5980 chunk 361 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN A 571 GLN F 23 ASN L 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089404 restraints weight = 44445.559| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.63 r_work: 0.2983 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30074 Z= 0.105 Angle : 0.499 9.778 40754 Z= 0.255 Chirality : 0.043 0.156 4567 Planarity : 0.004 0.050 5336 Dihedral : 5.346 158.723 4199 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.88 % Allowed : 15.31 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.14), residues: 3761 helix: 1.82 (0.14), residues: 1548 sheet: 0.07 (0.21), residues: 586 loop : -0.05 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 130 TYR 0.012 0.001 TYR G 133 PHE 0.017 0.001 PHE A 230 TRP 0.016 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (30074) covalent geometry : angle 0.49859 / 0.25 (40754) hydrogen bonds : bond 0.04084 / 2.77 ( 1269) hydrogen bonds : angle 4.33955 / 3.04 ( 3618) *********************** 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 328 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8371 (ptpp) cc_final: 0.7807 (mttp) REVERT: A 154 ARG cc_start: 0.7874 (ptm160) cc_final: 0.7272 (ptt90) REVERT: A 323 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7896 (mtt) REVERT: A 416 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8010 (ttm-80) REVERT: A 502 GLU cc_start: 0.8065 (pm20) cc_final: 0.7761 (mp0) REVERT: A 524 LYS cc_start: 0.8598 (ptmt) cc_final: 0.7974 (mttt) REVERT: A 547 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7385 (ttt90) REVERT: A 550 ARG cc_start: 0.8217 (mmt90) cc_final: 0.7196 (mtp-110) REVERT: B 170 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7428 (tp30) REVERT: B 314 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7682 (ptt90) REVERT: B 408 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8387 (ttt-90) REVERT: B 467 ILE cc_start: 0.7037 (mm) cc_final: 0.6764 (mt) REVERT: B 502 GLU cc_start: 0.8580 (tt0) cc_final: 0.8104 (mp0) REVERT: B 567 MET cc_start: 0.7914 (tpt) cc_final: 0.7624 (tpt) REVERT: C 1 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6598 (mmt) REVERT: C 46 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8856 (p) REVERT: C 124 LYS cc_start: 0.8319 (mppt) cc_final: 0.7668 (mmmt) REVERT: C 202 ASN cc_start: 0.9096 (p0) cc_final: 0.8847 (p0) REVERT: C 323 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.7978 (mmt) REVERT: C 441 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: C 480 GLU cc_start: 0.6765 (pt0) cc_final: 0.6431 (pm20) REVERT: C 532 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5390 (mtp85) REVERT: C 550 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7662 (ttm-80) REVERT: D 416 ASP cc_start: 0.8459 (m-30) cc_final: 0.8191 (m-30) REVERT: E 410 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7077 (ttt90) REVERT: F 7 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7396 (mp0) REVERT: G 137 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7143 (mt) REVERT: G 148 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7248 (mttp) REVERT: G 149 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7310 (mtpt) REVERT: H 91 ARG cc_start: 0.6504 (mmm160) cc_final: 0.5858 (mmp80) REVERT: J 80 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.5283 (mm) REVERT: J 105 ARG cc_start: 0.5051 (mtt90) cc_final: 0.4755 (ttm110) REVERT: J 148 LEU cc_start: 0.2789 (tp) cc_final: 0.2468 (pp) REVERT: J 164 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5358 (tp30) REVERT: J 172 ASP cc_start: 0.5782 (m-30) cc_final: 0.5332 (OUTLIER) REVERT: K 91 ARG cc_start: 0.4675 (ttm170) cc_final: 0.4364 (mtp85) REVERT: L 184 GLN cc_start: 0.6070 (tt0) cc_final: 0.5795 (tm130) outliers start: 58 outliers final: 21 residues processed: 315 average time/residue: 0.8368 time to fit residues: 301.5403 Evaluate side-chains 288 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 282 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 335 optimal weight: 20.0000 chunk 283 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 300 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN A 571 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.087959 restraints weight = 44656.404| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.67 r_work: 0.2960 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30074 Z= 0.144 Angle : 0.527 8.347 40754 Z= 0.270 Chirality : 0.044 0.158 4567 Planarity : 0.005 0.049 5336 Dihedral : 5.279 146.737 4199 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.98 % Allowed : 15.54 % Favored : 82.48 % 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: 1.07 (0.14), residues: 3761 helix: 1.81 (0.14), residues: 1557 sheet: 0.11 (0.22), residues: 580 loop : -0.06 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 453 TYR 0.013 0.001 TYR H 89 PHE 0.015 0.001 PHE C 559 TRP 0.014 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (30074) covalent geometry : angle 0.52743 / 0.27 (40754) hydrogen bonds : bond 0.04584 / 3.10 ( 1269) hydrogen bonds : angle 4.36523 / 3.06 ( 3618) *********************** 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 325 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8354 (ptpp) cc_final: 0.7853 (mttp) REVERT: A 154 ARG cc_start: 0.7859 (ptm160) cc_final: 0.7249 (ptt90) REVERT: A 323 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.7942 (mtt) REVERT: A 416 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8063 (ttm-80) REVERT: A 502 GLU cc_start: 0.8061 (pm20) cc_final: 0.7759 (mp0) REVERT: A 524 LYS cc_start: 0.8587 (ptmt) cc_final: 0.7974 (mttt) REVERT: A 547 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7409 (ttt90) REVERT: A 550 ARG cc_start: 0.8217 (mmt90) cc_final: 0.7239 (mtp-110) REVERT: B 1 MET cc_start: 0.7120 (ttm) cc_final: 0.6887 (ttm) REVERT: B 170 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: B 314 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7793 (ptt90) REVERT: B 408 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.8416 (ttt-90) REVERT: B 467 ILE cc_start: 0.6977 (mm) cc_final: 0.6686 (mt) REVERT: B 502 GLU cc_start: 0.8625 (tt0) cc_final: 0.8104 (mp0) REVERT: B 567 MET cc_start: 0.7909 (tpt) cc_final: 0.7575 (tpt) REVERT: C 46 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8890 (p) REVERT: C 124 LYS cc_start: 0.8326 (mppt) cc_final: 0.7674 (mmmt) REVERT: C 323 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7999 (mmt) REVERT: C 441 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 470 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5791 (tp) REVERT: C 532 ARG cc_start: 0.5777 (OUTLIER) cc_final: 0.5440 (mtp85) REVERT: C 550 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.7717 (ttm-80) REVERT: D 413 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: E 410 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7121 (ttt90) REVERT: E 442 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8149 (mt) REVERT: F 7 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7434 (mp0) REVERT: F 391 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: G 137 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7196 (mt) REVERT: G 148 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7385 (mttp) REVERT: G 149 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7520 (mppt) REVERT: H 91 ARG cc_start: 0.6524 (mmm160) cc_final: 0.5876 (mmp80) REVERT: J 80 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5242 (mm) REVERT: J 105 ARG cc_start: 0.4927 (mtt90) cc_final: 0.4637 (ttm110) REVERT: J 148 LEU cc_start: 0.2807 (tp) cc_final: 0.2466 (pp) REVERT: J 164 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5368 (tp30) REVERT: J 172 ASP cc_start: 0.5745 (m-30) cc_final: 0.5289 (m-30) REVERT: K 91 ARG cc_start: 0.4666 (ttm170) cc_final: 0.4359 (mtp85) REVERT: K 117 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: L 184 GLN cc_start: 0.6094 (tt0) cc_final: 0.5820 (tm130) outliers start: 61 outliers final: 25 residues processed: 313 average time/residue: 0.8308 time to fit residues: 298.3481 Evaluate side-chains 294 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 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: 10.0000 chunk 256 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 249 optimal weight: 0.5980 chunk 250 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 372 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN A 571 GLN F 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088942 restraints weight = 44457.987| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.69 r_work: 0.2977 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30074 Z= 0.114 Angle : 0.505 10.492 40754 Z= 0.257 Chirality : 0.043 0.192 4567 Planarity : 0.004 0.049 5336 Dihedral : 4.948 125.687 4199 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.75 % Allowed : 15.64 % Favored : 82.61 % 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: 1.20 (0.14), residues: 3761 helix: 1.90 (0.14), residues: 1561 sheet: 0.16 (0.22), residues: 575 loop : 0.03 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 453 TYR 0.014 0.001 TYR H 89 PHE 0.014 0.001 PHE A 230 TRP 0.015 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (30074) covalent geometry : angle 0.50462 / 0.26 (40754) hydrogen bonds : bond 0.04131 / 2.80 ( 1269) hydrogen bonds : angle 4.27535 / 2.99 ( 3618) *********************** 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 315 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8361 (ptpp) cc_final: 0.7882 (mttp) REVERT: A 154 ARG cc_start: 0.7876 (ptm160) cc_final: 0.7275 (ptt90) REVERT: A 323 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7898 (mtt) REVERT: A 416 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8054 (ttm-80) REVERT: A 502 GLU cc_start: 0.8062 (pm20) cc_final: 0.7760 (mp0) REVERT: A 524 LYS cc_start: 0.8589 (ptmt) cc_final: 0.7972 (mttt) REVERT: A 547 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7356 (ttt90) REVERT: A 550 ARG cc_start: 0.8212 (mmt90) cc_final: 0.7243 (mtp-110) REVERT: B 170 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: B 314 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7839 (ptt90) REVERT: B 408 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8392 (ttt-90) REVERT: B 467 ILE cc_start: 0.6969 (mm) cc_final: 0.6679 (mt) REVERT: B 502 GLU cc_start: 0.8590 (tt0) cc_final: 0.8090 (mp0) REVERT: B 567 MET cc_start: 0.7914 (tpt) cc_final: 0.7584 (tpt) REVERT: C 46 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8889 (p) REVERT: C 124 LYS cc_start: 0.8350 (mppt) cc_final: 0.7708 (mmmt) REVERT: C 323 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8005 (mmt) REVERT: C 441 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: C 532 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.5405 (mtp85) REVERT: C 550 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.7659 (ttm-80) REVERT: D 413 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8353 (mp10) REVERT: E 410 ARG cc_start: 0.7411 (ttm110) cc_final: 0.7075 (ttt90) REVERT: G 148 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7324 (mttp) REVERT: G 149 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7521 (mppt) REVERT: H 91 ARG cc_start: 0.6459 (mmm160) cc_final: 0.5825 (mmp80) REVERT: J 80 LEU cc_start: 0.5436 (OUTLIER) cc_final: 0.5185 (mm) REVERT: J 105 ARG cc_start: 0.4852 (mtt90) cc_final: 0.4558 (ttm110) REVERT: J 110 GLU cc_start: 0.6682 (tp30) cc_final: 0.6481 (tp30) REVERT: J 148 LEU cc_start: 0.2752 (tp) cc_final: 0.2441 (pp) REVERT: J 164 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5351 (tp30) REVERT: J 172 ASP cc_start: 0.5649 (m-30) cc_final: 0.5195 (m-30) REVERT: K 91 ARG cc_start: 0.4607 (ttm170) cc_final: 0.4302 (mtp85) REVERT: K 104 MET cc_start: 0.5702 (ttm) cc_final: 0.5226 (ttp) REVERT: K 117 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: L 184 GLN cc_start: 0.6152 (tt0) cc_final: 0.5872 (tm130) outliers start: 54 outliers final: 27 residues processed: 306 average time/residue: 0.7503 time to fit residues: 264.4593 Evaluate side-chains 290 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 337 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 chunk 358 optimal weight: 20.0000 chunk 254 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 336 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 295 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN A 541 GLN A 571 GLN F 23 ASN L 165 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.088017 restraints weight = 44399.664| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.74 r_work: 0.2953 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30074 Z= 0.138 Angle : 0.527 8.763 40754 Z= 0.268 Chirality : 0.043 0.201 4567 Planarity : 0.005 0.068 5336 Dihedral : 4.896 108.911 4199 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.69 % Allowed : 15.83 % Favored : 82.48 % 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: 1.15 (0.14), residues: 3761 helix: 1.85 (0.14), residues: 1561 sheet: 0.16 (0.22), residues: 575 loop : 0.01 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 453 TYR 0.012 0.001 TYR H 89 PHE 0.015 0.001 PHE C 559 TRP 0.014 0.001 TRP A 119 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (30074) covalent geometry : angle 0.52738 / 0.27 (40754) hydrogen bonds : bond 0.04467 / 3.02 ( 1269) hydrogen bonds : angle 4.32377 / 3.03 ( 3618) ********************** 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 306 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8344 (ptpp) cc_final: 0.7874 (mttp) REVERT: A 154 ARG cc_start: 0.7880 (ptm160) cc_final: 0.7253 (ptt90) REVERT: A 323 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7945 (mtt) REVERT: A 416 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8075 (ttm-80) REVERT: A 502 GLU cc_start: 0.8050 (pm20) cc_final: 0.7753 (mp0) REVERT: A 524 LYS cc_start: 0.8596 (ptmt) cc_final: 0.7967 (mttt) REVERT: A 547 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7353 (ttt90) REVERT: A 550 ARG cc_start: 0.8216 (mmt90) cc_final: 0.7244 (mtp-110) REVERT: B 1 MET cc_start: 0.6983 (ttm) cc_final: 0.6511 (ttp) REVERT: B 170 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: B 314 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7776 (ptt90) REVERT: B 408 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8403 (ttt-90) REVERT: B 467 ILE cc_start: 0.6919 (mm) cc_final: 0.6620 (mt) REVERT: B 502 GLU cc_start: 0.8617 (tt0) cc_final: 0.8075 (mp0) REVERT: B 547 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.7177 (mpp-170) REVERT: C 46 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8900 (p) REVERT: C 124 LYS cc_start: 0.8356 (mppt) cc_final: 0.7693 (mmmt) REVERT: C 323 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8006 (mmt) REVERT: C 441 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: C 532 ARG cc_start: 0.5661 (OUTLIER) cc_final: 0.5377 (mtp85) REVERT: C 550 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.7661 (ttm-80) REVERT: D 413 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8345 (mp10) REVERT: D 416 ASP cc_start: 0.8464 (m-30) cc_final: 0.8202 (m-30) REVERT: E 410 ARG cc_start: 0.7456 (ttm110) cc_final: 0.7118 (ttt90) REVERT: G 137 LEU cc_start: 0.7853 (tp) cc_final: 0.7638 (mt) REVERT: G 148 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7343 (mttp) REVERT: G 149 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7508 (mppt) REVERT: H 91 ARG cc_start: 0.6472 (mmm160) cc_final: 0.5825 (mmp80) REVERT: J 80 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.5262 (mm) REVERT: J 105 ARG cc_start: 0.4850 (mtt90) cc_final: 0.4561 (ttm110) REVERT: J 148 LEU cc_start: 0.2831 (tp) cc_final: 0.2526 (pp) REVERT: J 164 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5359 (tp30) REVERT: J 172 ASP cc_start: 0.5670 (m-30) cc_final: 0.5203 (m-30) REVERT: K 91 ARG cc_start: 0.4695 (ttm170) cc_final: 0.4362 (mtp85) REVERT: K 117 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: L 134 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4781 (tm) REVERT: L 184 GLN cc_start: 0.6156 (tt0) cc_final: 0.5872 (tm130) outliers start: 52 outliers final: 31 residues processed: 297 average time/residue: 0.7943 time to fit residues: 272.3583 Evaluate side-chains 295 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 532 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 317 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 95 optimal weight: 0.0980 chunk 141 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 217 optimal weight: 0.0980 chunk 191 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 286 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN A 541 GLN A 571 GLN G 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088054 restraints weight = 44701.692| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.73 r_work: 0.2960 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.256 30074 Z= 0.205 Angle : 0.733 61.584 40754 Z= 0.377 Chirality : 0.049 1.359 4567 Planarity : 0.005 0.207 5336 Dihedral : 4.922 108.819 4199 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.65 % Allowed : 16.16 % Favored : 82.19 % Cbeta Deviations : 0.06 % 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: 1.13 (0.14), residues: 3761 helix: 1.83 (0.14), residues: 1561 sheet: 0.15 (0.22), residues: 575 loop : 0.00 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 130 TYR 0.012 0.001 TYR H 89 PHE 0.015 0.001 PHE C 559 TRP 0.014 0.001 TRP A 119 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (30074) covalent geometry : angle 0.73328 / 0.38 (40754) hydrogen bonds : bond 0.04557 / 3.09 ( 1269) hydrogen bonds : angle 4.33013 / 3.03 ( 3618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10938.52 seconds wall clock time: 186 minutes 33.10 seconds (11193.10 seconds total)