Starting phenix.real_space_refine on Sat Feb 7 01:00:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vat_31863/02_2026/7vat_31863.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vat_31863/02_2026/7vat_31863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vat_31863/02_2026/7vat_31863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vat_31863/02_2026/7vat_31863.map" model { file = "/net/cci-nas-00/data/ceres_data/7vat_31863/02_2026/7vat_31863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vat_31863/02_2026/7vat_31863.cif" } resolution = 3.2 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29520 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4467 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 981 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.73, per 1000 atoms: 0.23 Number of scatterers: 29520 At special positions: 0 Unit cell: (139.04, 177.76, 153.12, 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: 2.52 Conformation dependent library (CDL) restraints added in 1.8 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: 151 helices and 25 sheets defined 48.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.021A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.498A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.559A pdb=" N ASP A 390 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.551A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.031A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.753A 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: 3.542A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.753A 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: 3.589A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.749A 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: 4.843A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.650A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.775A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) removed outlier: 3.530A 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 472 Processing helix chain 'B' and resid 473 through 476 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: 3.609A 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: 3.654A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.889A 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 259 through 269 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: 4.204A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 4.173A 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 415 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.125A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.842A 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: 3.736A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 4.274A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.587A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 removed outlier: 3.531A pdb=" N MET D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.576A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.932A 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: 3.659A 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: 3.937A pdb=" N VAL D 366 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.515A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.346A 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: 4.085A 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: 3.887A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.591A pdb=" N LEU E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.226A 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: 3.701A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.787A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.531A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.174A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (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: 3.526A pdb=" N LEU E 451 " --> pdb=" O GLN E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 removed outlier: 3.835A pdb=" N LYS E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.589A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.576A pdb=" N GLU F 230 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 275 removed outlier: 3.939A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.179A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR F 283 " --> pdb=" O ARG F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 279 through 283' Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.756A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 removed outlier: 3.519A pdb=" N ASP F 320 " --> pdb=" O PRO F 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 317 through 320' Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 374 through 399 Processing helix chain 'F' and resid 400 through 404 removed outlier: 3.541A pdb=" N ALA F 403 " --> pdb=" O GLY F 400 " (cutoff:3.500A) 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: 3.744A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 4.350A 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 68 removed outlier: 3.808A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.545A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.527A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 208 Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 25 through 40 Processing helix chain 'H' and resid 54 through 58 Processing helix chain 'H' and resid 59 through 64 removed outlier: 4.586A pdb=" N ARG H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.750A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 83 through 104 removed outlier: 4.286A pdb=" N ARG I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.686A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 removed outlier: 3.794A 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: 3.613A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 5.610A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.571A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 105 removed outlier: 4.099A pdb=" N TYR K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 removed outlier: 3.667A pdb=" N GLU K 117 " --> pdb=" O LEU K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.563A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.498A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.507A 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: 6.464A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.110A 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: 5.729A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.633A 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) removed outlier: 3.673A pdb=" N ASP A 43 " --> pdb=" O THR A 46 " (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: 6.526A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.817A 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: 5.754A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.748A 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: 6.646A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.125A 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: 5.918A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.623A 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: 5.845A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.556A 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: 3.858A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.506A 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 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 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 383 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 383 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 6.481A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.535A 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: 3.573A pdb=" N GLY B 155 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 148 removed outlier: 3.714A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.643A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.601A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.681A pdb=" N ARG D 91 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU D 221 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.686A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.373A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 124 through 125 removed outlier: 4.768A pdb=" N VAL E 300 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.632A 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: 3.641A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.509A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LYS F 223 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.735A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.555A pdb=" N VAL H 3 " --> pdb=" O GLU H 19 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA H 2 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP H 48 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE H 4 " --> pdb=" O ASP H 48 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1311 hydrogen bonds defined for protein. 3729 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: 5.81 Time building geometry restraints manager: 3.42 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: 9963 1.34 - 1.46: 4682 1.46 - 1.57: 15226 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30074 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.586 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C8 ADP A 601 " pdb=" N7 ADP A 601 " ideal model delta sigma weight residual 1.350 1.310 0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C5 ADP A 601 " pdb=" N7 ADP A 601 " ideal model delta sigma weight residual 1.350 1.387 -0.037 2.00e-02 2.50e+03 3.37e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 40651 3.23 - 6.46: 91 6.46 - 9.69: 9 9.69 - 12.92: 1 12.92 - 16.15: 2 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 120.50 136.65 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 119.90 106.95 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" N VAL B 503 " pdb=" CA VAL B 503 " pdb=" C VAL B 503 " ideal model delta sigma weight residual 113.53 110.19 3.34 9.80e-01 1.04e+00 1.16e+01 angle pdb=" C GLN G 166 " pdb=" N VAL G 167 " pdb=" CA VAL G 167 " ideal model delta sigma weight residual 123.16 119.56 3.60 1.06e+00 8.90e-01 1.15e+01 angle pdb=" N ILE D 96 " pdb=" CA ILE D 96 " pdb=" C ILE D 96 " ideal model delta sigma weight residual 111.88 108.49 3.39 1.06e+00 8.90e-01 1.02e+01 ... (remaining 40749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.96: 17379 22.96 - 45.92: 841 45.92 - 68.88: 87 68.88 - 91.84: 41 91.84 - 114.80: 1 Dihedral angle restraints: 18349 sinusoidal: 7531 harmonic: 10818 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -174.79 114.80 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N MET B 24 " pdb=" CA MET B 24 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 18346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3022 0.034 - 0.068: 1009 0.068 - 0.101: 352 0.101 - 0.135: 177 0.135 - 0.169: 7 Chirality restraints: 4567 Sorted by residual: chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA VAL E 21 " pdb=" N VAL E 21 " pdb=" C VAL E 21 " pdb=" CB VAL E 21 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL C 149 " pdb=" N VAL C 149 " pdb=" C VAL C 149 " pdb=" CB VAL C 149 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 4564 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 124 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO L 125 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 125 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 125 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO E 324 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 226 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 227 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.022 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 158 2.58 - 3.16: 23480 3.16 - 3.74: 44795 3.74 - 4.32: 62428 4.32 - 4.90: 106997 Nonbonded interactions: 237858 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.997 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.016 2.170 nonbonded pdb=" OE1 GLU D 109 " pdb=" OH TYR D 244 " model vdw 2.143 3.040 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.162 3.040 nonbonded pdb=" O LEU B 241 " pdb=" OG SER B 245 " model vdw 2.202 3.040 ... (remaining 237853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 through 578)) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.350 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.630 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 0.104 30074 Z= 0.144 Angle : 0.529 16.148 40754 Z= 0.278 Chirality : 0.042 0.169 4567 Planarity : 0.004 0.053 5336 Dihedral : 13.430 114.796 11433 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.37 (0.14), residues: 3761 helix: 1.94 (0.14), residues: 1553 sheet: 0.45 (0.23), residues: 552 loop : 0.17 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.009 0.001 TYR A 562 PHE 0.016 0.001 PHE G 130 TRP 0.008 0.001 TRP B 119 HIS 0.006 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00315 (30074) covalent geometry : angle 0.52864 (40754) hydrogen bonds : bond 0.15876 ( 1311) hydrogen bonds : angle 5.88742 ( 3729) *********************** 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 595 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8522 (tttt) cc_final: 0.8119 (tttm) REVERT: A 45 ASP cc_start: 0.7789 (t0) cc_final: 0.7549 (t0) REVERT: A 124 LYS cc_start: 0.7709 (ptpp) cc_final: 0.7471 (mmtm) REVERT: A 133 MET cc_start: 0.7960 (mtt) cc_final: 0.7756 (mtt) REVERT: A 235 SER cc_start: 0.7881 (t) cc_final: 0.7346 (p) REVERT: A 240 SER cc_start: 0.8007 (t) cc_final: 0.7761 (p) REVERT: A 480 GLU cc_start: 0.7207 (mp0) cc_final: 0.6589 (mp0) REVERT: A 557 GLU cc_start: 0.6949 (mp0) cc_final: 0.6746 (pt0) REVERT: B 133 MET cc_start: 0.7504 (mtt) cc_final: 0.7261 (mtp) REVERT: B 138 VAL cc_start: 0.7923 (t) cc_final: 0.7473 (m) REVERT: B 154 ARG cc_start: 0.6907 (mtp180) cc_final: 0.6075 (ttm110) REVERT: B 156 ARG cc_start: 0.7581 (ptm-80) cc_final: 0.7361 (ptm160) REVERT: B 159 GLU cc_start: 0.7064 (pt0) cc_final: 0.6595 (tt0) REVERT: B 160 VAL cc_start: 0.8281 (p) cc_final: 0.8007 (t) REVERT: B 169 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7367 (tp30) REVERT: B 417 ARG cc_start: 0.7373 (mpp-170) cc_final: 0.7080 (mmm160) REVERT: B 446 ASP cc_start: 0.6112 (p0) cc_final: 0.5806 (p0) REVERT: B 467 ILE cc_start: 0.6958 (mm) cc_final: 0.6517 (tt) REVERT: B 550 ARG cc_start: 0.7123 (mmm160) cc_final: 0.6898 (mmp80) REVERT: C 93 ARG cc_start: 0.7572 (mmp80) cc_final: 0.7111 (mmm-85) REVERT: C 183 MET cc_start: 0.9215 (mtt) cc_final: 0.8791 (mtm) REVERT: C 197 ARG cc_start: 0.7462 (ttp-110) cc_final: 0.7192 (ttp80) REVERT: C 209 MET cc_start: 0.8257 (mtp) cc_final: 0.8010 (mtp) REVERT: C 277 THR cc_start: 0.6894 (m) cc_final: 0.6665 (p) REVERT: C 416 ARG cc_start: 0.7402 (mtm110) cc_final: 0.7149 (mtp180) REVERT: C 425 ASN cc_start: 0.7858 (t0) cc_final: 0.7627 (t0) REVERT: C 441 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6765 (mm-30) REVERT: C 481 ARG cc_start: 0.7600 (mtp180) cc_final: 0.7366 (mtm180) REVERT: C 489 ILE cc_start: 0.8199 (mt) cc_final: 0.7576 (tp) REVERT: C 492 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7575 (mm-30) REVERT: C 546 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7255 (tm-30) REVERT: C 569 GLU cc_start: 0.7098 (tt0) cc_final: 0.6630 (tt0) REVERT: C 570 ILE cc_start: 0.8265 (mt) cc_final: 0.8019 (mt) REVERT: D 280 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7382 (mtp180) REVERT: D 380 ASP cc_start: 0.7376 (p0) cc_final: 0.7082 (t0) REVERT: D 402 ASP cc_start: 0.7007 (p0) cc_final: 0.6777 (p0) REVERT: D 437 GLN cc_start: 0.7667 (tt0) cc_final: 0.7461 (tt0) REVERT: E 81 ARG cc_start: 0.8194 (mpt-90) cc_final: 0.7921 (mtt-85) REVERT: E 210 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7411 (ttp-170) REVERT: E 342 GLU cc_start: 0.7078 (tp30) cc_final: 0.6767 (tp30) REVERT: F 7 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7058 (tt0) REVERT: F 36 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8014 (mtpt) REVERT: F 202 SER cc_start: 0.8355 (t) cc_final: 0.8114 (m) REVERT: F 248 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6895 (mt-10) REVERT: F 353 ASP cc_start: 0.8125 (t0) cc_final: 0.7675 (t70) REVERT: F 362 MET cc_start: 0.8775 (ttt) cc_final: 0.8574 (ttt) REVERT: F 388 ASN cc_start: 0.8085 (m-40) cc_final: 0.7782 (m-40) REVERT: F 391 ASP cc_start: 0.7544 (m-30) cc_final: 0.7292 (m-30) REVERT: F 465 GLN cc_start: 0.6097 (tm-30) cc_final: 0.5521 (pm20) REVERT: G 9 MET cc_start: 0.7652 (ttp) cc_final: 0.7336 (ttp) REVERT: G 31 LYS cc_start: 0.6442 (tttt) cc_final: 0.6128 (tttt) REVERT: G 148 LYS cc_start: 0.7492 (mmtp) cc_final: 0.7217 (mttt) REVERT: H 1 MET cc_start: 0.2720 (mmm) cc_final: 0.2279 (tmm) REVERT: H 36 LEU cc_start: 0.5524 (mt) cc_final: 0.5257 (tt) REVERT: H 90 MET cc_start: 0.5823 (mmt) cc_final: 0.5269 (mmp) REVERT: H 97 THR cc_start: 0.4727 (m) cc_final: 0.4506 (t) REVERT: J 110 GLU cc_start: 0.5885 (tp30) cc_final: 0.5017 (tt0) REVERT: J 126 GLU cc_start: 0.4916 (tt0) cc_final: 0.4336 (mm-30) REVERT: J 145 GLU cc_start: 0.5544 (tt0) cc_final: 0.5325 (tt0) REVERT: L 82 GLU cc_start: 0.5107 (tp30) cc_final: 0.4816 (tt0) REVERT: L 88 ARG cc_start: 0.5330 (ttp-170) cc_final: 0.5094 (ttp-170) REVERT: L 112 LEU cc_start: 0.7097 (mt) cc_final: 0.6465 (tp) REVERT: L 119 LYS cc_start: 0.6463 (pttt) cc_final: 0.6127 (pttm) REVERT: L 132 GLU cc_start: 0.5577 (tp30) cc_final: 0.5249 (mm-30) REVERT: L 136 ARG cc_start: 0.4838 (mmp80) cc_final: 0.4510 (ptt180) REVERT: L 138 ARG cc_start: 0.4832 (mmm160) cc_final: 0.3646 (ptp-170) REVERT: L 148 LEU cc_start: 0.3850 (tp) cc_final: 0.3592 (tp) REVERT: L 172 ASP cc_start: 0.7293 (m-30) cc_final: 0.6881 (m-30) REVERT: L 173 ARG cc_start: 0.4642 (mmm160) cc_final: 0.4259 (mtm110) REVERT: L 175 TRP cc_start: 0.6507 (t-100) cc_final: 0.6230 (t-100) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.2259 time to fit residues: 197.3527 Evaluate side-chains 348 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 397 GLN C 145 HIS C 423 ASN D 249 HIS D 364 ASN E 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089621 restraints weight = 45244.115| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.03 r_work: 0.2893 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 30074 Z= 0.228 Angle : 0.628 8.955 40754 Z= 0.324 Chirality : 0.048 0.158 4567 Planarity : 0.006 0.061 5336 Dihedral : 5.889 106.326 4230 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.14 % Allowed : 6.52 % Favored : 92.34 % 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: 0.84 (0.14), residues: 3761 helix: 1.50 (0.13), residues: 1564 sheet: 0.09 (0.22), residues: 565 loop : -0.11 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.014 0.002 TYR H 21 PHE 0.017 0.002 PHE E 130 TRP 0.022 0.002 TRP A 119 HIS 0.015 0.002 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00554 (30074) covalent geometry : angle 0.62834 (40754) hydrogen bonds : bond 0.06000 ( 1311) hydrogen bonds : angle 4.89474 ( 3729) *********************** 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 369 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 334 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9079 (tttt) cc_final: 0.8863 (tttm) REVERT: A 124 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7785 (mmtm) REVERT: A 197 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8319 (mtm-85) REVERT: A 240 SER cc_start: 0.8516 (t) cc_final: 0.8262 (p) REVERT: A 375 GLU cc_start: 0.8130 (tt0) cc_final: 0.7913 (mt-10) REVERT: A 480 GLU cc_start: 0.7562 (mp0) cc_final: 0.7186 (mp0) REVERT: A 527 GLU cc_start: 0.7841 (tt0) cc_final: 0.7635 (mm-30) REVERT: B 17 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8342 (pttm) REVERT: B 81 ASN cc_start: 0.8913 (t0) cc_final: 0.8694 (t0) REVERT: B 138 VAL cc_start: 0.8631 (t) cc_final: 0.8376 (m) REVERT: B 159 GLU cc_start: 0.7437 (pt0) cc_final: 0.7026 (tt0) REVERT: B 160 VAL cc_start: 0.8303 (p) cc_final: 0.8092 (t) REVERT: B 246 ASN cc_start: 0.7495 (m110) cc_final: 0.7266 (m110) REVERT: B 417 ARG cc_start: 0.8130 (mpp-170) cc_final: 0.7728 (mmm160) REVERT: B 446 ASP cc_start: 0.6508 (p0) cc_final: 0.6186 (p0) REVERT: B 460 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7315 (mtm180) REVERT: C 93 ARG cc_start: 0.8255 (mmp80) cc_final: 0.7847 (mmm-85) REVERT: C 197 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7799 (ttp80) REVERT: C 416 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7942 (mtp180) REVERT: C 441 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7245 (mm-30) REVERT: C 492 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8174 (mm-30) REVERT: C 540 LEU cc_start: 0.7525 (mp) cc_final: 0.7165 (tp) REVERT: C 546 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7767 (tm-30) REVERT: D 410 ARG cc_start: 0.7083 (mmm-85) cc_final: 0.6852 (mtp180) REVERT: D 437 GLN cc_start: 0.8211 (tt0) cc_final: 0.8003 (tt0) REVERT: E 373 GLU cc_start: 0.7992 (pt0) cc_final: 0.7555 (tp30) REVERT: F 248 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7721 (mt-10) REVERT: F 391 ASP cc_start: 0.8571 (m-30) cc_final: 0.8312 (m-30) REVERT: F 465 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6449 (pt0) REVERT: G 17 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8471 (mm110) REVERT: G 131 ARG cc_start: 0.5423 (mtm-85) cc_final: 0.4744 (mtt-85) REVERT: G 148 LYS cc_start: 0.7968 (mmtp) cc_final: 0.7623 (mttt) REVERT: H 1 MET cc_start: 0.3265 (mmm) cc_final: 0.2830 (tmm) REVERT: J 110 GLU cc_start: 0.5990 (tp30) cc_final: 0.5589 (tt0) REVERT: J 126 GLU cc_start: 0.5177 (tt0) cc_final: 0.4522 (mm-30) REVERT: J 145 GLU cc_start: 0.5489 (tt0) cc_final: 0.5198 (tt0) REVERT: L 92 GLU cc_start: 0.5594 (mm-30) cc_final: 0.5020 (tp30) REVERT: L 119 LYS cc_start: 0.6924 (pttt) cc_final: 0.6506 (pttp) REVERT: L 132 GLU cc_start: 0.5304 (tp30) cc_final: 0.4908 (mm-30) REVERT: L 136 ARG cc_start: 0.4782 (mmp80) cc_final: 0.4569 (ptt180) REVERT: L 148 LEU cc_start: 0.3861 (tp) cc_final: 0.3631 (tp) REVERT: L 172 ASP cc_start: 0.7617 (m-30) cc_final: 0.7227 (m-30) REVERT: L 173 ARG cc_start: 0.4989 (mmm160) cc_final: 0.4765 (mtp-110) REVERT: L 175 TRP cc_start: 0.7005 (t-100) cc_final: 0.6566 (t-100) outliers start: 35 outliers final: 24 residues processed: 357 average time/residue: 0.2186 time to fit residues: 117.4532 Evaluate side-chains 306 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 220 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN E 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.089524 restraints weight = 45330.378| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.92 r_work: 0.2885 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30074 Z= 0.216 Angle : 0.604 9.804 40754 Z= 0.311 Chirality : 0.047 0.165 4567 Planarity : 0.005 0.066 5336 Dihedral : 5.886 91.213 4230 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.75 % Allowed : 9.38 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3761 helix: 1.34 (0.13), residues: 1567 sheet: -0.19 (0.22), residues: 554 loop : -0.34 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.020 0.002 TYR H 21 PHE 0.015 0.002 PHE A 230 TRP 0.022 0.002 TRP A 119 HIS 0.013 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00529 (30074) covalent geometry : angle 0.60412 (40754) hydrogen bonds : bond 0.05691 ( 1311) hydrogen bonds : angle 4.76158 ( 3729) *********************** 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 339 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 0.886 Fit side-chains REVERT: A 8 LYS cc_start: 0.9094 (tttt) cc_final: 0.8888 (tttm) REVERT: A 15 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9046 (mm) REVERT: A 124 LYS cc_start: 0.8017 (ptpp) cc_final: 0.7791 (mmtm) REVERT: A 197 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.8330 (mtm-85) REVERT: A 375 GLU cc_start: 0.8093 (tt0) cc_final: 0.7856 (mt-10) REVERT: A 480 GLU cc_start: 0.7496 (mp0) cc_final: 0.7144 (mp0) REVERT: A 527 GLU cc_start: 0.7817 (tt0) cc_final: 0.7616 (mm-30) REVERT: A 546 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7134 (mm-30) REVERT: B 17 LYS cc_start: 0.8543 (ptmt) cc_final: 0.8318 (pttm) REVERT: B 137 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7947 (m) REVERT: B 138 VAL cc_start: 0.8789 (t) cc_final: 0.8470 (m) REVERT: B 154 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.6921 (ttm110) REVERT: B 159 GLU cc_start: 0.7352 (pt0) cc_final: 0.6899 (tt0) REVERT: B 393 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6514 (tm-30) REVERT: B 417 ARG cc_start: 0.8083 (mpp-170) cc_final: 0.7692 (mmm160) REVERT: B 422 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8860 (mp) REVERT: B 460 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7301 (mtm180) REVERT: B 488 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7762 (ttp-170) REVERT: C 93 ARG cc_start: 0.8295 (mmp80) cc_final: 0.7851 (mmm-85) REVERT: C 197 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7842 (ttp80) REVERT: C 344 MET cc_start: 0.8595 (ttm) cc_final: 0.8369 (ttp) REVERT: C 416 ARG cc_start: 0.8108 (mtm110) cc_final: 0.7758 (mtp85) REVERT: C 492 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8214 (mm-30) REVERT: C 546 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7767 (tm-30) REVERT: C 568 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7732 (mttp) REVERT: D 334 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: D 410 ARG cc_start: 0.7075 (mmm-85) cc_final: 0.6845 (mtp180) REVERT: E 334 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8363 (mt-10) REVERT: F 248 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7680 (mt-10) REVERT: F 452 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8441 (tptp) REVERT: F 465 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6401 (pt0) REVERT: G 17 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8468 (mm110) REVERT: G 148 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7605 (mttt) REVERT: H 1 MET cc_start: 0.3173 (mmm) cc_final: 0.2767 (ttt) REVERT: J 110 GLU cc_start: 0.5982 (tp30) cc_final: 0.5635 (tt0) REVERT: J 126 GLU cc_start: 0.5189 (tt0) cc_final: 0.4487 (mm-30) REVERT: J 145 GLU cc_start: 0.5495 (tt0) cc_final: 0.5151 (tt0) REVERT: L 119 LYS cc_start: 0.7115 (pttt) cc_final: 0.6830 (pttm) REVERT: L 138 ARG cc_start: 0.5909 (tpp-160) cc_final: 0.5496 (mmt-90) REVERT: L 172 ASP cc_start: 0.7740 (m-30) cc_final: 0.7343 (m-30) REVERT: L 175 TRP cc_start: 0.7034 (t-100) cc_final: 0.6596 (t-100) outliers start: 54 outliers final: 36 residues processed: 321 average time/residue: 0.2051 time to fit residues: 101.3537 Evaluate side-chains 304 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 330 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 364 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 368 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN F 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090575 restraints weight = 44893.886| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.88 r_work: 0.2922 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30074 Z= 0.169 Angle : 0.549 9.618 40754 Z= 0.283 Chirality : 0.045 0.150 4567 Planarity : 0.005 0.065 5336 Dihedral : 5.690 87.252 4230 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.72 % Allowed : 11.13 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3761 helix: 1.54 (0.13), residues: 1567 sheet: -0.18 (0.23), residues: 548 loop : -0.31 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.016 0.001 TYR H 21 PHE 0.014 0.001 PHE A 230 TRP 0.021 0.001 TRP A 119 HIS 0.010 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00407 (30074) covalent geometry : angle 0.54930 (40754) hydrogen bonds : bond 0.05016 ( 1311) hydrogen bonds : angle 4.59761 ( 3729) *********************** 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 336 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 1.284 Fit side-chains REVERT: A 8 LYS cc_start: 0.9089 (tttt) cc_final: 0.8875 (ttpt) REVERT: A 15 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9011 (mm) REVERT: A 375 GLU cc_start: 0.7982 (tt0) cc_final: 0.7754 (mt-10) REVERT: A 480 GLU cc_start: 0.7454 (mp0) cc_final: 0.7157 (mp0) REVERT: A 527 GLU cc_start: 0.7807 (tt0) cc_final: 0.7571 (mm-30) REVERT: A 546 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7083 (mm-30) REVERT: B 17 LYS cc_start: 0.8515 (ptmt) cc_final: 0.8293 (pttm) REVERT: B 138 VAL cc_start: 0.8783 (t) cc_final: 0.8488 (m) REVERT: B 154 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.6950 (ttm110) REVERT: B 393 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6425 (tm-30) REVERT: B 417 ARG cc_start: 0.8033 (mpp-170) cc_final: 0.7679 (mmm160) REVERT: B 446 ASP cc_start: 0.6170 (p0) cc_final: 0.5893 (p0) REVERT: B 488 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7709 (ttp-170) REVERT: C 93 ARG cc_start: 0.8242 (mmp80) cc_final: 0.7857 (mmm-85) REVERT: C 344 MET cc_start: 0.8528 (ttm) cc_final: 0.8318 (ttp) REVERT: C 416 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7680 (mtp85) REVERT: C 492 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8097 (mm-30) REVERT: C 546 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7763 (tm-30) REVERT: D 57 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8696 (mp) REVERT: D 410 ARG cc_start: 0.7030 (mmm-85) cc_final: 0.6813 (mtp180) REVERT: E 373 GLU cc_start: 0.7996 (pt0) cc_final: 0.7600 (tp30) REVERT: E 445 MET cc_start: 0.8570 (ttm) cc_final: 0.8021 (mtp) REVERT: F 248 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7586 (mt-10) REVERT: F 452 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8359 (tptp) REVERT: F 465 GLN cc_start: 0.7293 (tm-30) cc_final: 0.6163 (pt0) REVERT: G 17 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8428 (mm110) REVERT: G 148 LYS cc_start: 0.8021 (mmtp) cc_final: 0.7604 (mttt) REVERT: H 90 MET cc_start: 0.6237 (mmt) cc_final: 0.5670 (mmm) REVERT: J 110 GLU cc_start: 0.5911 (tp30) cc_final: 0.5613 (tt0) REVERT: J 126 GLU cc_start: 0.5207 (tt0) cc_final: 0.4509 (mm-30) REVERT: J 145 GLU cc_start: 0.5503 (tt0) cc_final: 0.5155 (tt0) REVERT: L 119 LYS cc_start: 0.7050 (pttt) cc_final: 0.6774 (pttm) REVERT: L 138 ARG cc_start: 0.5926 (tpp-160) cc_final: 0.5280 (mmt-90) REVERT: L 172 ASP cc_start: 0.7702 (m-30) cc_final: 0.7294 (m-30) REVERT: L 175 TRP cc_start: 0.6938 (t-100) cc_final: 0.6507 (t-100) outliers start: 53 outliers final: 40 residues processed: 317 average time/residue: 0.2184 time to fit residues: 106.1732 Evaluate side-chains 307 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 100 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 327 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS F 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.090106 restraints weight = 45246.674| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.82 r_work: 0.2915 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30074 Z= 0.188 Angle : 0.572 9.526 40754 Z= 0.294 Chirality : 0.046 0.152 4567 Planarity : 0.005 0.077 5336 Dihedral : 5.722 81.533 4230 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.30 % Allowed : 11.81 % Favored : 85.89 % 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: 0.56 (0.14), residues: 3761 helix: 1.45 (0.13), residues: 1557 sheet: -0.27 (0.22), residues: 567 loop : -0.37 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.017 0.001 TYR H 21 PHE 0.014 0.002 PHE C 559 TRP 0.022 0.002 TRP A 119 HIS 0.010 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00459 (30074) covalent geometry : angle 0.57176 (40754) hydrogen bonds : bond 0.05214 ( 1311) hydrogen bonds : angle 4.60893 ( 3729) *********************** 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 336 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 265 time to evaluate : 1.234 Fit side-chains REVERT: A 8 LYS cc_start: 0.9090 (tttt) cc_final: 0.8866 (tttm) REVERT: A 15 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9039 (mm) REVERT: A 375 GLU cc_start: 0.7975 (tt0) cc_final: 0.7774 (mt-10) REVERT: A 480 GLU cc_start: 0.7445 (mp0) cc_final: 0.7233 (mp0) REVERT: A 546 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7121 (mm-30) REVERT: B 17 LYS cc_start: 0.8514 (ptmt) cc_final: 0.8290 (pttm) REVERT: B 137 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7973 (m) REVERT: B 154 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.6906 (ttm110) REVERT: B 156 ARG cc_start: 0.8046 (ptm-80) cc_final: 0.7780 (ptm160) REVERT: B 393 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6396 (tm-30) REVERT: B 417 ARG cc_start: 0.7956 (mpp-170) cc_final: 0.7643 (mmm160) REVERT: B 422 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8814 (mp) REVERT: B 446 ASP cc_start: 0.6278 (p0) cc_final: 0.5935 (p0) REVERT: B 488 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7740 (ttp-170) REVERT: C 93 ARG cc_start: 0.8247 (mmp80) cc_final: 0.7866 (mmm-85) REVERT: C 416 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7667 (mtp85) REVERT: C 492 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8118 (mm-30) REVERT: C 546 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7820 (tm-30) REVERT: D 57 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8714 (mp) REVERT: D 334 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: D 410 ARG cc_start: 0.6959 (mmm-85) cc_final: 0.6744 (mtp180) REVERT: E 334 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: E 373 GLU cc_start: 0.7995 (pt0) cc_final: 0.7652 (tp30) REVERT: E 445 MET cc_start: 0.8536 (ttm) cc_final: 0.8038 (mtp) REVERT: F 248 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7554 (mt-10) REVERT: F 452 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8372 (tptp) REVERT: G 17 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8433 (mm110) REVERT: G 148 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7585 (mttt) REVERT: H 1 MET cc_start: 0.3540 (mmt) cc_final: 0.2172 (tmm) REVERT: J 110 GLU cc_start: 0.5862 (tp30) cc_final: 0.5648 (tt0) REVERT: J 126 GLU cc_start: 0.5437 (tt0) cc_final: 0.4730 (mm-30) REVERT: J 145 GLU cc_start: 0.5530 (tt0) cc_final: 0.5169 (tt0) REVERT: J 150 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5930 (tt) REVERT: K 91 ARG cc_start: 0.4712 (ttm170) cc_final: 0.4110 (tpp80) REVERT: L 84 ARG cc_start: 0.5104 (ttt-90) cc_final: 0.4896 (mmm160) REVERT: L 96 GLN cc_start: 0.4966 (mm110) cc_final: 0.4533 (mp10) REVERT: L 119 LYS cc_start: 0.7066 (pttt) cc_final: 0.6675 (pttp) REVERT: L 172 ASP cc_start: 0.7647 (m-30) cc_final: 0.7136 (m-30) REVERT: L 175 TRP cc_start: 0.6989 (t-100) cc_final: 0.6747 (t-100) outliers start: 71 outliers final: 55 residues processed: 319 average time/residue: 0.2091 time to fit residues: 102.9967 Evaluate side-chains 319 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 103 VAL 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: 0.0050 chunk 238 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.090077 restraints weight = 44970.451| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.84 r_work: 0.2904 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30074 Z= 0.182 Angle : 0.561 9.668 40754 Z= 0.289 Chirality : 0.045 0.147 4567 Planarity : 0.005 0.066 5336 Dihedral : 5.679 80.220 4230 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.47 % Allowed : 12.69 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.57 (0.14), residues: 3761 helix: 1.50 (0.13), residues: 1558 sheet: -0.28 (0.22), residues: 563 loop : -0.39 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.016 0.001 TYR H 21 PHE 0.015 0.002 PHE A 230 TRP 0.021 0.001 TRP A 119 HIS 0.009 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00445 (30074) covalent geometry : angle 0.56146 (40754) hydrogen bonds : bond 0.05092 ( 1311) hydrogen bonds : angle 4.57915 ( 3729) *********************** 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 341 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9131 (tttt) cc_final: 0.8916 (tttm) REVERT: A 15 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9037 (mm) REVERT: A 375 GLU cc_start: 0.8058 (tt0) cc_final: 0.7835 (mt-10) REVERT: A 480 GLU cc_start: 0.7507 (mp0) cc_final: 0.7293 (mp0) REVERT: A 546 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 17 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8309 (pttm) REVERT: B 137 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7805 (m) REVERT: B 154 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.6902 (ttm110) REVERT: B 393 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: B 417 ARG cc_start: 0.8040 (mpp-170) cc_final: 0.7697 (mmm160) REVERT: B 422 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8845 (mp) REVERT: B 446 ASP cc_start: 0.6383 (p0) cc_final: 0.6029 (p0) REVERT: B 488 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.7831 (ttp-170) REVERT: C 93 ARG cc_start: 0.8295 (mmp80) cc_final: 0.7904 (mmm-85) REVERT: C 416 ARG cc_start: 0.8036 (mtm110) cc_final: 0.7759 (mpt180) REVERT: C 492 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8178 (mm-30) REVERT: C 546 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7865 (tm-30) REVERT: C 568 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7842 (mttp) REVERT: D 57 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8686 (mp) REVERT: D 334 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: D 410 ARG cc_start: 0.6977 (mmm-85) cc_final: 0.6706 (mtp180) REVERT: E 334 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: E 373 GLU cc_start: 0.8077 (pt0) cc_final: 0.7687 (tp30) REVERT: E 445 MET cc_start: 0.8546 (ttm) cc_final: 0.8057 (mtp) REVERT: F 248 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7565 (mt-10) REVERT: F 452 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8402 (tptp) REVERT: G 17 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8490 (mm110) REVERT: G 148 LYS cc_start: 0.8054 (mmtp) cc_final: 0.7640 (mttt) REVERT: H 1 MET cc_start: 0.3472 (mmt) cc_final: 0.2247 (tmm) REVERT: J 145 GLU cc_start: 0.5604 (tt0) cc_final: 0.5229 (tt0) REVERT: K 91 ARG cc_start: 0.4790 (ttm170) cc_final: 0.4170 (tpp80) REVERT: L 96 GLN cc_start: 0.5044 (mm110) cc_final: 0.4664 (mp10) REVERT: L 119 LYS cc_start: 0.7050 (pttt) cc_final: 0.6674 (pttp) REVERT: L 172 ASP cc_start: 0.7645 (m-30) cc_final: 0.7089 (m-30) outliers start: 76 outliers final: 60 residues processed: 325 average time/residue: 0.2152 time to fit residues: 107.9699 Evaluate side-chains 322 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 255 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 75 optimal weight: 0.5980 chunk 202 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 chunk 361 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092832 restraints weight = 44786.579| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.92 r_work: 0.2948 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30074 Z= 0.100 Angle : 0.486 15.951 40754 Z= 0.247 Chirality : 0.042 0.151 4567 Planarity : 0.004 0.059 5336 Dihedral : 5.255 78.482 4230 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.59 % Allowed : 13.79 % Favored : 84.62 % 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: 1.01 (0.14), residues: 3761 helix: 1.90 (0.14), residues: 1564 sheet: -0.10 (0.23), residues: 560 loop : -0.20 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.007 0.001 TYR D 13 PHE 0.013 0.001 PHE C 230 TRP 0.018 0.001 TRP A 119 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00218 (30074) covalent geometry : angle 0.48566 (40754) hydrogen bonds : bond 0.03958 ( 1311) hydrogen bonds : angle 4.34365 ( 3729) *********************** 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 327 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 278 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9137 (tttt) cc_final: 0.8893 (ttpt) REVERT: A 154 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7829 (ptm-80) REVERT: A 375 GLU cc_start: 0.8020 (tt0) cc_final: 0.7796 (mt-10) REVERT: A 450 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 546 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7132 (mm-30) REVERT: B 17 LYS cc_start: 0.8463 (ptmt) cc_final: 0.8231 (pttm) REVERT: B 154 ARG cc_start: 0.7692 (ttp-170) cc_final: 0.6906 (ttm110) REVERT: B 156 ARG cc_start: 0.7949 (ptm-80) cc_final: 0.7625 (ptm160) REVERT: B 269 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7949 (t80) REVERT: B 315 ASP cc_start: 0.8003 (m-30) cc_final: 0.7778 (m-30) REVERT: B 393 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6355 (tm-30) REVERT: B 417 ARG cc_start: 0.8011 (mpp-170) cc_final: 0.7688 (mmm160) REVERT: B 422 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8854 (mp) REVERT: B 488 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7712 (ttp-170) REVERT: C 1 MET cc_start: 0.6681 (mmm) cc_final: 0.6448 (mmt) REVERT: C 93 ARG cc_start: 0.8238 (mmp80) cc_final: 0.7989 (mmm-85) REVERT: C 416 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7700 (mpt180) REVERT: C 492 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8150 (mm-30) REVERT: C 546 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7814 (tm-30) REVERT: D 57 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8699 (mp) REVERT: D 334 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: E 334 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: E 373 GLU cc_start: 0.8020 (pt0) cc_final: 0.7656 (tp30) REVERT: E 445 MET cc_start: 0.8507 (ttm) cc_final: 0.7974 (mtp) REVERT: F 248 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7461 (mt-10) REVERT: F 452 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8463 (tptp) REVERT: G 17 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8371 (mm-40) REVERT: G 148 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7597 (mttt) REVERT: H 90 MET cc_start: 0.6244 (mmm) cc_final: 0.5754 (mmm) REVERT: I 119 LEU cc_start: 0.3817 (OUTLIER) cc_final: 0.2948 (pp) REVERT: J 145 GLU cc_start: 0.5615 (tt0) cc_final: 0.5279 (tt0) REVERT: K 116 LYS cc_start: 0.6625 (pttp) cc_final: 0.6306 (pptt) REVERT: L 96 GLN cc_start: 0.5093 (mm110) cc_final: 0.4738 (mp10) REVERT: L 119 LYS cc_start: 0.7066 (pttt) cc_final: 0.6828 (pttm) REVERT: L 128 LEU cc_start: 0.4700 (pp) cc_final: 0.4286 (mt) REVERT: L 172 ASP cc_start: 0.7551 (m-30) cc_final: 0.7081 (m-30) outliers start: 49 outliers final: 24 residues processed: 316 average time/residue: 0.2036 time to fit residues: 99.6257 Evaluate side-chains 287 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 282 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 335 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 300 optimal weight: 0.0060 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090534 restraints weight = 45150.280| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.85 r_work: 0.2921 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2945 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= 0.185 Angle : 0.571 13.602 40754 Z= 0.290 Chirality : 0.045 0.177 4567 Planarity : 0.005 0.056 5336 Dihedral : 5.537 79.473 4230 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.78 % Allowed : 13.76 % Favored : 84.46 % 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: 0.76 (0.14), residues: 3761 helix: 1.65 (0.13), residues: 1561 sheet: -0.13 (0.23), residues: 560 loop : -0.31 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.013 0.001 TYR H 21 PHE 0.016 0.002 PHE A 230 TRP 0.019 0.002 TRP A 119 HIS 0.009 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00450 (30074) covalent geometry : angle 0.57057 (40754) hydrogen bonds : bond 0.04993 ( 1311) hydrogen bonds : angle 4.50550 ( 3729) *********************** 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 300 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8596 (mmp80) cc_final: 0.8339 (mmp80) REVERT: A 375 GLU cc_start: 0.7976 (tt0) cc_final: 0.7766 (mt-10) REVERT: A 546 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7013 (mm-30) REVERT: B 17 LYS cc_start: 0.8478 (ptmt) cc_final: 0.8233 (pttm) REVERT: B 154 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.6911 (ttm110) REVERT: B 269 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8024 (t80) REVERT: B 393 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6341 (tm-30) REVERT: B 417 ARG cc_start: 0.7982 (mpp-170) cc_final: 0.7693 (mmm160) REVERT: B 422 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 488 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7791 (ttp-170) REVERT: C 93 ARG cc_start: 0.8264 (mmp80) cc_final: 0.7924 (mmm-85) REVERT: C 416 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7640 (mtp85) REVERT: C 492 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8086 (mm-30) REVERT: C 546 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7851 (tm-30) REVERT: C 568 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7784 (mttp) REVERT: D 57 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8673 (mp) REVERT: D 334 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: D 410 ARG cc_start: 0.6970 (mmm-85) cc_final: 0.6728 (mtp180) REVERT: E 334 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: E 373 GLU cc_start: 0.8002 (pt0) cc_final: 0.7651 (tp30) REVERT: G 17 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8420 (mm110) REVERT: G 148 LYS cc_start: 0.8086 (mmtp) cc_final: 0.7625 (mttt) REVERT: H 90 MET cc_start: 0.6285 (mmm) cc_final: 0.5765 (mmm) REVERT: I 119 LEU cc_start: 0.3758 (OUTLIER) cc_final: 0.2884 (pp) REVERT: J 145 GLU cc_start: 0.5608 (tt0) cc_final: 0.5283 (tt0) REVERT: J 150 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5937 (tt) REVERT: K 91 ARG cc_start: 0.4779 (ttm170) cc_final: 0.4213 (tpp80) REVERT: K 116 LYS cc_start: 0.6572 (pttp) cc_final: 0.6275 (pptt) REVERT: L 96 GLN cc_start: 0.5218 (mm110) cc_final: 0.4859 (mp10) REVERT: L 119 LYS cc_start: 0.7058 (pttt) cc_final: 0.6702 (pttp) REVERT: L 172 ASP cc_start: 0.7560 (m-30) cc_final: 0.7082 (m-30) outliers start: 55 outliers final: 43 residues processed: 288 average time/residue: 0.2226 time to fit residues: 99.0082 Evaluate side-chains 292 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 250 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 372 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 296 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN F 166 GLN F 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.093291 restraints weight = 44793.636| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.84 r_work: 0.2968 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30074 Z= 0.102 Angle : 0.491 13.289 40754 Z= 0.249 Chirality : 0.042 0.164 4567 Planarity : 0.004 0.055 5336 Dihedral : 5.174 78.276 4230 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.27 % Allowed : 14.41 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3761 helix: 1.91 (0.14), residues: 1565 sheet: -0.04 (0.23), residues: 560 loop : -0.16 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 547 TYR 0.009 0.001 TYR D 383 PHE 0.013 0.001 PHE C 230 TRP 0.018 0.001 TRP A 119 HIS 0.005 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00225 (30074) covalent geometry : angle 0.49127 (40754) hydrogen bonds : bond 0.03916 ( 1311) hydrogen bonds : angle 4.30586 ( 3729) *********************** 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 291 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 154 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7824 (ptm-80) REVERT: B 17 LYS cc_start: 0.8410 (ptmt) cc_final: 0.8183 (pttm) REVERT: B 154 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.6883 (ttm110) REVERT: B 269 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7883 (t80) REVERT: B 315 ASP cc_start: 0.7948 (m-30) cc_final: 0.7683 (m-30) REVERT: B 393 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6261 (tm-30) REVERT: B 417 ARG cc_start: 0.7956 (mpp-170) cc_final: 0.7745 (mmm160) REVERT: B 422 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8837 (mp) REVERT: B 488 ARG cc_start: 0.8106 (ttp-110) cc_final: 0.7670 (ttp-170) REVERT: C 416 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7672 (mpt180) REVERT: C 492 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8093 (mm-30) REVERT: C 568 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7706 (mttp) REVERT: D 57 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8672 (mp) REVERT: D 334 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: E 334 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: E 373 GLU cc_start: 0.7975 (pt0) cc_final: 0.7637 (tp30) REVERT: F 248 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7324 (mt-10) REVERT: G 17 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8325 (mm-40) REVERT: G 148 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7565 (mttt) REVERT: H 90 MET cc_start: 0.6277 (mmm) cc_final: 0.5787 (mmm) REVERT: I 119 LEU cc_start: 0.3766 (OUTLIER) cc_final: 0.2900 (pp) REVERT: J 145 GLU cc_start: 0.5594 (tt0) cc_final: 0.5261 (tt0) REVERT: K 116 LYS cc_start: 0.6591 (pttp) cc_final: 0.6211 (pptt) REVERT: L 96 GLN cc_start: 0.5225 (mm110) cc_final: 0.4776 (mp10) REVERT: L 119 LYS cc_start: 0.6981 (pttt) cc_final: 0.6667 (pttp) REVERT: L 172 ASP cc_start: 0.7528 (m-30) cc_final: 0.7056 (m-30) outliers start: 39 outliers final: 26 residues processed: 280 average time/residue: 0.2081 time to fit residues: 90.0876 Evaluate side-chains 272 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 337 optimal weight: 0.3980 chunk 232 optimal weight: 8.9990 chunk 358 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 336 optimal weight: 7.9990 chunk 253 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 81 optimal weight: 9.9990 chunk 295 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.093387 restraints weight = 44670.426| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.83 r_work: 0.2964 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30074 Z= 0.100 Angle : 0.485 13.135 40754 Z= 0.246 Chirality : 0.042 0.164 4567 Planarity : 0.004 0.055 5336 Dihedral : 5.056 81.516 4230 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.04 % Allowed : 14.63 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3761 helix: 1.97 (0.14), residues: 1566 sheet: 0.07 (0.23), residues: 545 loop : -0.10 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 547 TYR 0.011 0.001 TYR F 54 PHE 0.013 0.001 PHE C 559 TRP 0.018 0.001 TRP A 119 HIS 0.005 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00223 (30074) covalent geometry : angle 0.48512 (40754) hydrogen bonds : bond 0.03770 ( 1311) hydrogen bonds : angle 4.25151 ( 3729) ********************** 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 286 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8193 (t0) REVERT: A 154 ARG cc_start: 0.8199 (ptm160) cc_final: 0.7862 (ptm-80) REVERT: B 17 LYS cc_start: 0.8435 (ptmt) cc_final: 0.8204 (pttm) REVERT: B 154 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.6896 (ttm110) REVERT: B 269 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7883 (t80) REVERT: B 315 ASP cc_start: 0.7954 (m-30) cc_final: 0.7693 (m-30) REVERT: B 393 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6357 (tm-30) REVERT: B 417 ARG cc_start: 0.8003 (mpp-170) cc_final: 0.7760 (mmm160) REVERT: B 422 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8862 (mp) REVERT: B 488 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7747 (ttp-170) REVERT: C 1 MET cc_start: 0.7167 (mmt) cc_final: 0.6868 (mmm) REVERT: C 416 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7644 (mtp85) REVERT: C 492 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8126 (mm-30) REVERT: C 568 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7641 (mttp) REVERT: D 57 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8681 (mp) REVERT: E 334 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: E 373 GLU cc_start: 0.7975 (pt0) cc_final: 0.7636 (tp30) REVERT: G 17 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8327 (mm-40) REVERT: G 148 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7595 (mttt) REVERT: H 87 GLU cc_start: 0.5359 (mp0) cc_final: 0.5134 (mm-30) REVERT: H 90 MET cc_start: 0.6257 (mmm) cc_final: 0.5759 (mmm) REVERT: I 119 LEU cc_start: 0.3714 (OUTLIER) cc_final: 0.2843 (pp) REVERT: J 145 GLU cc_start: 0.5454 (tt0) cc_final: 0.5172 (tt0) REVERT: K 116 LYS cc_start: 0.6533 (pttp) cc_final: 0.6161 (pptt) REVERT: L 96 GLN cc_start: 0.5258 (mm110) cc_final: 0.4865 (mp10) REVERT: L 119 LYS cc_start: 0.6971 (pttt) cc_final: 0.6657 (pttp) REVERT: L 172 ASP cc_start: 0.7580 (m-30) cc_final: 0.7095 (m-30) outliers start: 32 outliers final: 23 residues processed: 280 average time/residue: 0.2164 time to fit residues: 93.8007 Evaluate side-chains 270 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 317 optimal weight: 10.0000 chunk 161 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 191 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.090097 restraints weight = 45300.676| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.76 r_work: 0.2918 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30074 Z= 0.234 Angle : 0.626 12.945 40754 Z= 0.320 Chirality : 0.048 0.169 4567 Planarity : 0.006 0.054 5336 Dihedral : 5.656 80.282 4230 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.65 % Allowed : 14.28 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3761 helix: 1.48 (0.13), residues: 1564 sheet: -0.22 (0.23), residues: 551 loop : -0.36 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 547 TYR 0.014 0.002 TYR H 21 PHE 0.016 0.002 PHE A 230 TRP 0.019 0.002 TRP A 119 HIS 0.010 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00581 (30074) covalent geometry : angle 0.62614 (40754) hydrogen bonds : bond 0.05438 ( 1311) hydrogen bonds : angle 4.58945 ( 3729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7574.11 seconds wall clock time: 129 minutes 57.96 seconds (7797.96 seconds total)