Starting phenix.real_space_refine on Fri Mar 6 08:03:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vak_31845/03_2026/7vak_31845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vak_31845/03_2026/7vak_31845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vak_31845/03_2026/7vak_31845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vak_31845/03_2026/7vak_31845.map" model { file = "/net/cci-nas-00/data/ceres_data/7vak_31845/03_2026/7vak_31845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vak_31845/03_2026/7vak_31845.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 18705 2.51 5 N 5116 2.21 5 O 5538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29462 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Time building chain proxies: 5.83, per 1000 atoms: 0.20 Number of scatterers: 29462 At special positions: 0 Unit cell: (149.6, 141.68, 182.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 5538 8.00 N 5116 7.00 C 18705 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: 2.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 28 sheets defined 46.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.940A pdb=" N ILE A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.531A pdb=" N PHE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.067A 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 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 298 through 316 Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.591A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 352 No H-bonds generated for 'chain 'A' and resid 351 through 352' Processing helix chain 'A' and resid 353 through 364 removed outlier: 3.811A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.590A pdb=" N ASP A 390 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.999A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.579A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 531 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.984A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.509A 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 216 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.785A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 295 through 317 removed outlier: 5.429A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 342 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: 3.750A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.592A pdb=" N VAL B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) 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 533 removed outlier: 3.723A pdb=" N ALA B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.869A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 550 through 554 removed outlier: 3.603A pdb=" N TYR B 553 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 550 through 554' Processing helix chain 'B' and resid 558 through 578 Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.765A pdb=" N ILE C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) 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 272 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 317 removed outlier: 4.508A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.503A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.314A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.565A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.515A pdb=" N ALA C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.838A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.580A pdb=" N ARG C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 removed outlier: 3.536A pdb=" N VAL C 554 " --> pdb=" O ALA C 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.524A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.562A pdb=" N MET D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.609A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.135A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.534A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 274 removed outlier: 3.566A pdb=" N ARG D 274 " --> pdb=" O ILE D 270 " (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 347 removed outlier: 3.785A pdb=" N HIS D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 397 removed outlier: 3.608A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.541A pdb=" N LEU D 404 " --> pdb=" O GLU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.594A pdb=" N ARG D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 468 through 473 removed outlier: 3.590A pdb=" N GLY D 472 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.713A pdb=" N MET E 88 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.685A pdb=" N ARG E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 141 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.670A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.566A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 229 through 250 removed outlier: 3.837A pdb=" N LEU E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.952A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.822A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 347 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.870A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 397 removed outlier: 3.614A pdb=" N VAL E 378 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL E 390 " --> pdb=" O TYR E 386 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.717A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.541A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 removed outlier: 3.707A pdb=" N ILE E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY E 460 " --> pdb=" O LYS E 456 " (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 178 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 213 through 217 removed outlier: 3.564A pdb=" N SER F 217 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.708A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 362 through 366 removed outlier: 3.933A pdb=" N VAL F 366 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.996A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (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 455 through 463 Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 70 removed outlier: 3.911A pdb=" N LEU G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS G 58 " --> pdb=" O ASP G 54 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 83 Processing helix chain 'G' and resid 122 through 209 removed outlier: 3.577A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 removed outlier: 4.225A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.986A pdb=" N GLU H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 63 removed outlier: 4.807A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 105 removed outlier: 4.077A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.728A pdb=" N LEU I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 removed outlier: 3.895A pdb=" N LEU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.663A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 131 removed outlier: 3.531A pdb=" N LEU J 128 " --> pdb=" O PRO J 125 " (cutoff:3.500A) Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.475A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.749A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 127 through 139 removed outlier: 3.893A pdb=" N LEU L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.057A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.452A 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: 6.512A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.402A 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: 7.011A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 47 through 51 current: chain 'B' and resid 35 through 43 removed outlier: 6.771A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.480A 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: 5.726A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 43 " --> pdb=" O THR C 46 " (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: 6.656A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 6.858A 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 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 42 through 51 removed outlier: 7.084A pdb=" N VAL E 56 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL E 50 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.774A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR F 54 " --> pdb=" O SER F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 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 151 through 155 removed outlier: 3.517A pdb=" N VAL L 152 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.575A pdb=" N TRP A 187 " --> pdb=" O VAL A 73 " (cutoff:3.500A) 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 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 288 current: chain 'A' and resid 375 through 382 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 382 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 117 through 119 removed outlier: 3.505A pdb=" N TRP A 117 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.753A 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 removed outlier: 3.588A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 140 removed outlier: 4.040A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA8, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.506A pdb=" N TRP B 187 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 current: chain 'B' and resid 375 through 383 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 383 current: chain 'B' and resid 422 through 429 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.961A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL B 160 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL B 172 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 140 removed outlier: 3.666A pdb=" N PHE B 143 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.653A pdb=" N VAL C 73 " --> pdb=" O TRP C 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP C 187 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing sheet with id=AB4, 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 383 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.595A pdb=" N TYR C 166 " --> pdb=" O TRP C 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.994A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 129 removed outlier: 4.011A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AB9, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.927A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.604A pdb=" N VAL D 190 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.546A pdb=" N LEU E 112 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.189A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 188 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.483A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 152 through 154 removed outlier: 5.908A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 335 through 336 Processing sheet with id=AC7, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC8, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.860A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 314 " --> pdb=" O ILE F 152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 91 through 96 Processing sheet with id=AD1, first strand: chain 'H' and resid 19 through 21 removed outlier: 3.650A pdb=" N TYR H 21 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA H 2 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA H 46 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3594 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: 5.07 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9944 1.34 - 1.46: 4173 1.46 - 1.57: 15704 1.57 - 1.69: 0 1.69 - 1.81: 194 Bond restraints: 30015 Sorted by residual: bond pdb=" C HIS C 418 " pdb=" N PHE C 419 " ideal model delta sigma weight residual 1.331 1.313 0.017 1.48e-02 4.57e+03 1.37e+00 bond pdb=" CG PRO A 420 " pdb=" CD PRO A 420 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.23e+00 bond pdb=" N LEU F 355 " pdb=" CA LEU F 355 " ideal model delta sigma weight residual 1.463 1.457 0.006 6.90e-03 2.10e+04 7.93e-01 bond pdb=" C HIS A 418 " pdb=" N PHE A 419 " ideal model delta sigma weight residual 1.331 1.307 0.024 2.83e-02 1.25e+03 7.49e-01 bond pdb=" CG GLU K 117 " pdb=" CD GLU K 117 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.40e-01 ... (remaining 30010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 40302 2.27 - 4.55: 305 4.55 - 6.82: 45 6.82 - 9.09: 2 9.09 - 11.36: 4 Bond angle restraints: 40658 Sorted by residual: angle pdb=" C HIS C 418 " pdb=" N PHE C 419 " pdb=" CA PHE C 419 " ideal model delta sigma weight residual 121.03 115.14 5.89 1.60e+00 3.91e-01 1.36e+01 angle pdb=" CA LEU L 148 " pdb=" CB LEU L 148 " pdb=" CG LEU L 148 " ideal model delta sigma weight residual 116.30 127.66 -11.36 3.50e+00 8.16e-02 1.05e+01 angle pdb=" C ILE E 352 " pdb=" N ASP E 353 " pdb=" CA ASP E 353 " ideal model delta sigma weight residual 120.97 111.77 9.20 2.84e+00 1.24e-01 1.05e+01 angle pdb=" CA LEU H 32 " pdb=" CB LEU H 32 " pdb=" CG LEU H 32 " ideal model delta sigma weight residual 116.30 126.83 -10.53 3.50e+00 8.16e-02 9.05e+00 angle pdb=" C MET B 19 " pdb=" N LEU B 20 " pdb=" CA LEU B 20 " ideal model delta sigma weight residual 120.82 125.28 -4.46 1.50e+00 4.44e-01 8.83e+00 ... (remaining 40653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 16660 17.76 - 35.52: 1373 35.52 - 53.29: 203 53.29 - 71.05: 48 71.05 - 88.81: 20 Dihedral angle restraints: 18304 sinusoidal: 7482 harmonic: 10822 Sorted by residual: dihedral pdb=" CA ARG K 87 " pdb=" C ARG K 87 " pdb=" N TYR K 88 " pdb=" CA TYR K 88 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA VAL G 167 " pdb=" C VAL G 167 " pdb=" N VAL G 168 " pdb=" CA VAL G 168 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP E 290 " pdb=" CB ASP E 290 " pdb=" CG ASP E 290 " pdb=" OD1 ASP E 290 " ideal model delta sinusoidal sigma weight residual -30.00 -86.84 56.84 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3032 0.035 - 0.070: 989 0.070 - 0.104: 405 0.104 - 0.139: 126 0.139 - 0.174: 8 Chirality restraints: 4560 Sorted by residual: chirality pdb=" CA ILE B 15 " pdb=" N ILE B 15 " pdb=" C ILE B 15 " pdb=" CB ILE B 15 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA ARG K 87 " pdb=" N ARG K 87 " pdb=" C ARG K 87 " pdb=" CB ARG K 87 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 4557 not shown) Planarity restraints: 5330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO E 324 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 229 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 161 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 162 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.023 5.00e-02 4.00e+02 ... (remaining 5327 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 514 2.67 - 3.23: 28745 3.23 - 3.79: 45630 3.79 - 4.34: 60164 4.34 - 4.90: 99895 Nonbonded interactions: 234948 Sorted by model distance: nonbonded pdb=" OG1 THR E 405 " pdb=" OD1 ASN E 407 " model vdw 2.115 3.040 nonbonded pdb=" OG SER B 535 " pdb=" OD1 ASP B 537 " model vdw 2.127 3.040 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR D 411 " pdb=" OE1 GLU D 450 " model vdw 2.167 3.040 nonbonded pdb=" O ARG C 547 " pdb=" OH TYR C 562 " model vdw 2.173 3.040 ... (remaining 234943 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' selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.670 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 0.031 30015 Z= 0.126 Angle : 0.546 11.365 40658 Z= 0.287 Chirality : 0.043 0.174 4560 Planarity : 0.004 0.053 5330 Dihedral : 13.320 88.809 11386 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.43 (0.14), residues: 3764 helix: 1.42 (0.14), residues: 1533 sheet: -0.16 (0.23), residues: 545 loop : -0.57 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 532 TYR 0.011 0.001 TYR D 331 PHE 0.021 0.001 PHE A 269 TRP 0.010 0.001 TRP J 100 HIS 0.007 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00267 (30015) covalent geometry : angle 0.54627 (40658) hydrogen bonds : bond 0.15379 ( 1244) hydrogen bonds : angle 6.20265 ( 3594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.8493 (t) cc_final: 0.8173 (m) REVERT: A 133 MET cc_start: 0.7337 (mtp) cc_final: 0.6781 (mmm) REVERT: A 152 ASP cc_start: 0.8234 (m-30) cc_final: 0.7710 (p0) REVERT: A 153 VAL cc_start: 0.8738 (t) cc_final: 0.8353 (m) REVERT: A 169 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7410 (mt-10) REVERT: A 175 LEU cc_start: 0.8084 (mt) cc_final: 0.7430 (tp) REVERT: A 179 THR cc_start: 0.8103 (m) cc_final: 0.7803 (p) REVERT: A 220 MET cc_start: 0.7902 (tpp) cc_final: 0.7477 (ttp) REVERT: A 239 GLN cc_start: 0.7643 (mt0) cc_final: 0.7384 (pt0) REVERT: A 262 MET cc_start: 0.6702 (mmt) cc_final: 0.6446 (mmt) REVERT: A 323 MET cc_start: 0.7384 (mmt) cc_final: 0.7109 (mmt) REVERT: A 498 ASN cc_start: 0.8164 (t0) cc_final: 0.7471 (t0) REVERT: B 133 MET cc_start: 0.6876 (mtp) cc_final: 0.6632 (tmm) REVERT: B 186 THR cc_start: 0.8384 (p) cc_final: 0.7952 (t) REVERT: B 264 ASP cc_start: 0.7597 (p0) cc_final: 0.7250 (t70) REVERT: B 344 MET cc_start: 0.8411 (ptp) cc_final: 0.7893 (ppp) REVERT: C 161 LYS cc_start: 0.7433 (mmtm) cc_final: 0.6777 (mmtp) REVERT: C 170 GLU cc_start: 0.8129 (tp30) cc_final: 0.7849 (tm-30) REVERT: C 183 MET cc_start: 0.8957 (mtt) cc_final: 0.8391 (mtp) REVERT: C 212 LEU cc_start: 0.7872 (mt) cc_final: 0.7623 (mt) REVERT: C 282 MET cc_start: 0.7983 (tpt) cc_final: 0.7534 (tpt) REVERT: C 427 SER cc_start: 0.8024 (m) cc_final: 0.7812 (t) REVERT: C 520 LEU cc_start: 0.8142 (mt) cc_final: 0.7893 (tt) REVERT: C 546 GLU cc_start: 0.7830 (mp0) cc_final: 0.7534 (tm-30) REVERT: C 548 ILE cc_start: 0.8752 (mt) cc_final: 0.8505 (mt) REVERT: D 142 ASN cc_start: 0.8778 (m-40) cc_final: 0.8539 (m110) REVERT: D 190 VAL cc_start: 0.8352 (t) cc_final: 0.7931 (p) REVERT: D 230 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8016 (mt-10) REVERT: D 253 VAL cc_start: 0.9013 (t) cc_final: 0.8715 (m) REVERT: D 259 ASP cc_start: 0.6759 (t0) cc_final: 0.6508 (t0) REVERT: D 260 MET cc_start: 0.8594 (mmm) cc_final: 0.8033 (mmm) REVERT: D 276 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7302 (pt0) REVERT: D 305 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8050 (tttm) REVERT: E 106 ILE cc_start: 0.6134 (pt) cc_final: 0.5754 (pt) REVERT: E 214 LEU cc_start: 0.7675 (mt) cc_final: 0.7161 (mt) REVERT: E 296 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7816 (tp30) REVERT: E 360 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6901 (mtp180) REVERT: E 401 GLU cc_start: 0.8274 (pp20) cc_final: 0.7943 (mp0) REVERT: E 420 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8062 (tpp-160) REVERT: F 4 LEU cc_start: 0.7227 (pt) cc_final: 0.6922 (tt) REVERT: F 11 ILE cc_start: 0.8857 (mm) cc_final: 0.8624 (mp) REVERT: F 35 ILE cc_start: 0.8621 (mt) cc_final: 0.8316 (mt) REVERT: F 88 MET cc_start: 0.7624 (ptm) cc_final: 0.7254 (ptm) REVERT: F 89 LEU cc_start: 0.7631 (mt) cc_final: 0.7177 (tp) REVERT: F 194 MET cc_start: 0.8032 (mtm) cc_final: 0.7753 (mpp) REVERT: F 269 GLU cc_start: 0.8667 (tt0) cc_final: 0.8097 (tt0) REVERT: F 275 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7420 (pt0) REVERT: F 327 ASP cc_start: 0.7956 (t0) cc_final: 0.7751 (t0) REVERT: F 349 TYR cc_start: 0.8032 (t80) cc_final: 0.7783 (t80) REVERT: G 145 THR cc_start: 0.8478 (t) cc_final: 0.8148 (p) REVERT: H 36 LEU cc_start: 0.6286 (tp) cc_final: 0.5840 (mm) REVERT: H 39 ARG cc_start: 0.6418 (ttp80) cc_final: 0.6186 (tmt170) REVERT: H 52 LEU cc_start: 0.5293 (pt) cc_final: 0.5071 (mp) REVERT: H 68 LEU cc_start: 0.4985 (tp) cc_final: 0.4731 (mm) REVERT: J 78 GLU cc_start: 0.7781 (tp30) cc_final: 0.7442 (mt-10) REVERT: J 84 ARG cc_start: 0.6172 (mtt180) cc_final: 0.5945 (ttp-110) REVERT: J 99 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6993 (pm20) REVERT: J 115 LEU cc_start: 0.5660 (mt) cc_final: 0.5457 (mt) REVERT: J 126 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7156 (mp0) REVERT: J 134 LEU cc_start: 0.6754 (mm) cc_final: 0.6462 (mt) REVERT: L 78 GLU cc_start: 0.7157 (tt0) cc_final: 0.6923 (mm-30) REVERT: L 88 ARG cc_start: 0.7107 (mtp-110) cc_final: 0.6530 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.2257 time to fit residues: 221.5771 Evaluate side-chains 288 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN C 316 GLN D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 262 ASN E 388 ASN F 437 GLN F 458 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.052823 restraints weight = 115857.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.053934 restraints weight = 73898.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.054728 restraints weight = 52179.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.055263 restraints weight = 40126.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.055650 restraints weight = 33302.663| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30015 Z= 0.159 Angle : 0.601 10.692 40658 Z= 0.306 Chirality : 0.045 0.177 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.250 19.983 4180 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % 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: 0.27 (0.14), residues: 3764 helix: 1.23 (0.14), residues: 1565 sheet: -0.08 (0.23), residues: 561 loop : -0.71 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG E 430 TYR 0.019 0.001 TYR E 331 PHE 0.020 0.002 PHE E 187 TRP 0.025 0.001 TRP J 100 HIS 0.005 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00359 (30015) covalent geometry : angle 0.60084 (40658) hydrogen bonds : bond 0.04338 ( 1244) hydrogen bonds : angle 5.03120 ( 3594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8249 (mmm) cc_final: 0.7284 (tpp) REVERT: A 133 MET cc_start: 0.7746 (mtp) cc_final: 0.7536 (mtt) REVERT: A 152 ASP cc_start: 0.8127 (m-30) cc_final: 0.7430 (p0) REVERT: A 169 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7159 (mt-10) REVERT: A 175 LEU cc_start: 0.8404 (mt) cc_final: 0.7573 (tp) REVERT: A 220 MET cc_start: 0.7989 (tpp) cc_final: 0.7429 (ttp) REVERT: A 239 GLN cc_start: 0.7441 (mt0) cc_final: 0.7165 (tt0) REVERT: A 498 ASN cc_start: 0.8189 (t0) cc_final: 0.7890 (t0) REVERT: A 550 ARG cc_start: 0.7176 (tpp-160) cc_final: 0.6967 (mmm160) REVERT: B 133 MET cc_start: 0.7605 (mtp) cc_final: 0.7151 (tmm) REVERT: B 186 THR cc_start: 0.8696 (p) cc_final: 0.8228 (t) REVERT: B 282 MET cc_start: 0.7881 (tpt) cc_final: 0.7579 (tpp) REVERT: C 38 GLU cc_start: 0.7557 (tt0) cc_final: 0.7299 (tt0) REVERT: C 183 MET cc_start: 0.8654 (mtt) cc_final: 0.8382 (mtp) REVERT: C 282 MET cc_start: 0.7733 (tpt) cc_final: 0.7333 (tpt) REVERT: C 498 ASN cc_start: 0.8630 (m-40) cc_final: 0.8291 (m-40) REVERT: C 504 ASP cc_start: 0.8092 (t0) cc_final: 0.7615 (t70) REVERT: C 520 LEU cc_start: 0.8293 (mt) cc_final: 0.7845 (tt) REVERT: D 142 ASN cc_start: 0.8779 (m-40) cc_final: 0.8575 (m110) REVERT: D 190 VAL cc_start: 0.8334 (t) cc_final: 0.7936 (p) REVERT: D 194 MET cc_start: 0.7503 (mtp) cc_final: 0.7269 (mtp) REVERT: D 237 MET cc_start: 0.8857 (mmm) cc_final: 0.8629 (mmm) REVERT: D 260 MET cc_start: 0.8836 (mmm) cc_final: 0.8464 (mmm) REVERT: D 276 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7173 (pt0) REVERT: E 411 TYR cc_start: 0.6099 (m-80) cc_final: 0.5642 (m-80) REVERT: E 420 ARG cc_start: 0.8463 (mtp180) cc_final: 0.8245 (tpp-160) REVERT: F 11 ILE cc_start: 0.8766 (mm) cc_final: 0.8542 (mp) REVERT: F 88 MET cc_start: 0.7577 (ptm) cc_final: 0.7366 (ptm) REVERT: F 89 LEU cc_start: 0.8258 (mt) cc_final: 0.7683 (tp) REVERT: F 269 GLU cc_start: 0.8676 (tt0) cc_final: 0.8221 (tt0) REVERT: F 316 MET cc_start: 0.8740 (mtm) cc_final: 0.8338 (mtp) REVERT: J 78 GLU cc_start: 0.7672 (tp30) cc_final: 0.7268 (mt-10) REVERT: J 126 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6997 (mp0) REVERT: L 110 GLU cc_start: 0.6386 (pt0) cc_final: 0.5263 (tt0) REVERT: L 172 ASP cc_start: 0.7716 (m-30) cc_final: 0.7329 (p0) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.1903 time to fit residues: 112.9939 Evaluate side-chains 225 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 40 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN J 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.049529 restraints weight = 120779.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.050595 restraints weight = 78153.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.051321 restraints weight = 55619.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.051849 restraints weight = 43164.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.052223 restraints weight = 35716.989| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 30015 Z= 0.341 Angle : 0.796 14.325 40658 Z= 0.408 Chirality : 0.051 0.221 4560 Planarity : 0.006 0.062 5330 Dihedral : 5.065 33.712 4180 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.47 (0.14), residues: 3764 helix: 0.65 (0.13), residues: 1560 sheet: -0.63 (0.22), residues: 559 loop : -1.07 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 66 TYR 0.031 0.003 TYR C 166 PHE 0.031 0.003 PHE D 60 TRP 0.025 0.002 TRP J 100 HIS 0.010 0.002 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00788 (30015) covalent geometry : angle 0.79588 (40658) hydrogen bonds : bond 0.05492 ( 1244) hydrogen bonds : angle 5.30246 ( 3594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8308 (mmm) cc_final: 0.7474 (tpp) REVERT: A 133 MET cc_start: 0.8082 (mtp) cc_final: 0.7716 (mtt) REVERT: A 220 MET cc_start: 0.7895 (tpp) cc_final: 0.7494 (ttp) REVERT: A 239 GLN cc_start: 0.7661 (mt0) cc_final: 0.7380 (tt0) REVERT: A 311 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7405 (tt0) REVERT: A 550 ARG cc_start: 0.7105 (tpp-160) cc_final: 0.6842 (mmm160) REVERT: B 62 GLU cc_start: 0.7406 (mp0) cc_final: 0.7198 (mp0) REVERT: B 133 MET cc_start: 0.7771 (mtp) cc_final: 0.7135 (tmm) REVERT: B 262 MET cc_start: 0.8553 (pmm) cc_final: 0.8336 (pmm) REVERT: B 264 ASP cc_start: 0.6786 (p0) cc_final: 0.6551 (p0) REVERT: B 282 MET cc_start: 0.8476 (tpt) cc_final: 0.8239 (tpp) REVERT: B 391 MET cc_start: 0.7063 (mmt) cc_final: 0.6436 (mmm) REVERT: C 38 GLU cc_start: 0.7808 (tt0) cc_final: 0.7597 (tt0) REVERT: C 114 GLU cc_start: 0.8045 (mp0) cc_final: 0.7646 (pm20) REVERT: C 183 MET cc_start: 0.8500 (mtt) cc_final: 0.8134 (mtp) REVERT: C 282 MET cc_start: 0.7794 (tpt) cc_final: 0.7122 (tpt) REVERT: C 520 LEU cc_start: 0.8485 (mt) cc_final: 0.7999 (tt) REVERT: D 190 VAL cc_start: 0.8419 (t) cc_final: 0.8127 (p) REVERT: D 194 MET cc_start: 0.7256 (mtm) cc_final: 0.6976 (mtp) REVERT: D 276 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7197 (pt0) REVERT: D 296 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7387 (mm-30) REVERT: E 88 MET cc_start: 0.7589 (mtt) cc_final: 0.7343 (mtt) REVERT: E 316 MET cc_start: 0.8642 (mtp) cc_final: 0.8079 (mtm) REVERT: E 411 TYR cc_start: 0.6098 (m-80) cc_final: 0.5881 (m-80) REVERT: E 420 ARG cc_start: 0.8525 (mtp180) cc_final: 0.8314 (tpp-160) REVERT: F 11 ILE cc_start: 0.8926 (mm) cc_final: 0.8646 (mp) REVERT: F 88 MET cc_start: 0.7583 (ptm) cc_final: 0.7207 (ptm) REVERT: F 89 LEU cc_start: 0.8545 (mt) cc_final: 0.8186 (tp) REVERT: F 139 ASP cc_start: 0.7850 (m-30) cc_final: 0.7109 (t0) REVERT: F 141 MET cc_start: 0.8762 (mtp) cc_final: 0.8423 (mtp) REVERT: F 194 MET cc_start: 0.8297 (mpp) cc_final: 0.7779 (mmm) REVERT: F 287 MET cc_start: 0.7139 (ttm) cc_final: 0.6915 (ttm) REVERT: G 144 GLU cc_start: 0.8484 (tt0) cc_final: 0.7954 (tm-30) REVERT: H 63 MET cc_start: 0.6169 (tmm) cc_final: 0.5652 (tmm) REVERT: I 104 MET cc_start: 0.6763 (ttp) cc_final: 0.6445 (ptp) REVERT: J 78 GLU cc_start: 0.7613 (tp30) cc_final: 0.7329 (mt-10) REVERT: J 126 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7204 (mp0) REVERT: L 84 ARG cc_start: 0.6358 (ttt180) cc_final: 0.5271 (ttp80) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1834 time to fit residues: 83.4535 Evaluate side-chains 205 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 10 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 338 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN C 290 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.051246 restraints weight = 117221.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052341 restraints weight = 75262.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053118 restraints weight = 53241.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.053657 restraints weight = 40921.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054023 restraints weight = 33970.426| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30015 Z= 0.142 Angle : 0.591 11.495 40658 Z= 0.300 Chirality : 0.045 0.175 4560 Planarity : 0.005 0.048 5330 Dihedral : 4.595 22.405 4180 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % 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: -0.10 (0.14), residues: 3764 helix: 0.98 (0.13), residues: 1560 sheet: -0.36 (0.23), residues: 513 loop : -0.92 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 88 TYR 0.012 0.001 TYR F 349 PHE 0.025 0.001 PHE A 269 TRP 0.014 0.001 TRP J 100 HIS 0.017 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00324 (30015) covalent geometry : angle 0.59079 (40658) hydrogen bonds : bond 0.04420 ( 1244) hydrogen bonds : angle 4.87880 ( 3594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8064 (mm) cc_final: 0.7361 (tp) REVERT: A 220 MET cc_start: 0.7858 (tpp) cc_final: 0.7444 (ttp) REVERT: A 239 GLN cc_start: 0.7606 (mt0) cc_final: 0.7362 (tt0) REVERT: A 311 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7295 (tt0) REVERT: A 498 ASN cc_start: 0.8211 (t0) cc_final: 0.8003 (t0) REVERT: A 550 ARG cc_start: 0.6989 (tpp-160) cc_final: 0.6772 (mmm160) REVERT: B 62 GLU cc_start: 0.7472 (mp0) cc_final: 0.7098 (mp0) REVERT: B 93 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: B 133 MET cc_start: 0.7729 (mtp) cc_final: 0.7085 (tmm) REVERT: B 282 MET cc_start: 0.8124 (tpt) cc_final: 0.7841 (tpp) REVERT: B 567 MET cc_start: 0.6916 (tpp) cc_final: 0.6689 (tpp) REVERT: C 183 MET cc_start: 0.8624 (mtt) cc_final: 0.8314 (mtp) REVERT: C 239 GLN cc_start: 0.8230 (mt0) cc_final: 0.7461 (mp10) REVERT: C 282 MET cc_start: 0.7594 (tpt) cc_final: 0.6930 (tpt) REVERT: C 520 LEU cc_start: 0.8404 (mt) cc_final: 0.7920 (tt) REVERT: D 142 ASN cc_start: 0.8380 (m110) cc_final: 0.8073 (m110) REVERT: D 190 VAL cc_start: 0.8365 (t) cc_final: 0.8068 (p) REVERT: D 259 ASP cc_start: 0.6832 (t0) cc_final: 0.6444 (t0) REVERT: D 260 MET cc_start: 0.9041 (mmm) cc_final: 0.8515 (mmm) REVERT: D 276 GLU cc_start: 0.7860 (mt-10) cc_final: 0.6791 (pt0) REVERT: D 296 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7499 (mm-30) REVERT: E 316 MET cc_start: 0.8540 (mtp) cc_final: 0.8066 (mtm) REVERT: E 411 TYR cc_start: 0.6070 (m-80) cc_final: 0.5715 (m-10) REVERT: F 11 ILE cc_start: 0.8765 (mm) cc_final: 0.8517 (mp) REVERT: F 88 MET cc_start: 0.7348 (ptm) cc_final: 0.6890 (ptm) REVERT: F 89 LEU cc_start: 0.8494 (mt) cc_final: 0.8105 (tp) REVERT: F 194 MET cc_start: 0.8136 (mpp) cc_final: 0.7717 (mmm) REVERT: F 287 MET cc_start: 0.6961 (ttm) cc_final: 0.6598 (ttm) REVERT: G 144 GLU cc_start: 0.8414 (tt0) cc_final: 0.7763 (tm-30) REVERT: H 63 MET cc_start: 0.6094 (tmm) cc_final: 0.5829 (tmm) REVERT: H 98 ILE cc_start: 0.8849 (tp) cc_final: 0.8575 (tp) REVERT: J 78 GLU cc_start: 0.7463 (tp30) cc_final: 0.7221 (mt-10) REVERT: J 126 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7208 (mp0) REVERT: L 84 ARG cc_start: 0.5954 (ttt90) cc_final: 0.5333 (ttp80) REVERT: L 110 GLU cc_start: 0.6417 (pt0) cc_final: 0.5185 (tt0) REVERT: L 172 ASP cc_start: 0.7502 (m-30) cc_final: 0.6756 (p0) outliers start: 1 outliers final: 1 residues processed: 300 average time/residue: 0.1782 time to fit residues: 86.3789 Evaluate side-chains 208 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 139 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 265 optimal weight: 0.0470 chunk 22 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 296 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 overall best weight: 2.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.063159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051695 restraints weight = 116866.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.052769 restraints weight = 74871.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.053564 restraints weight = 53258.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.054118 restraints weight = 40917.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054456 restraints weight = 33633.026| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30015 Z= 0.140 Angle : 0.571 10.541 40658 Z= 0.291 Chirality : 0.044 0.170 4560 Planarity : 0.004 0.047 5330 Dihedral : 4.409 22.794 4180 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: 0.01 (0.14), residues: 3764 helix: 1.13 (0.13), residues: 1568 sheet: -0.44 (0.23), residues: 537 loop : -0.88 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 410 TYR 0.012 0.001 TYR F 463 PHE 0.019 0.001 PHE A 269 TRP 0.034 0.001 TRP A 330 HIS 0.007 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00321 (30015) covalent geometry : angle 0.57127 (40658) hydrogen bonds : bond 0.04119 ( 1244) hydrogen bonds : angle 4.74429 ( 3594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.7939 (mm) cc_final: 0.7278 (tp) REVERT: A 220 MET cc_start: 0.7866 (tpp) cc_final: 0.7503 (ttp) REVERT: A 311 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7370 (tt0) REVERT: A 391 MET cc_start: 0.8016 (mmm) cc_final: 0.7488 (tpp) REVERT: A 498 ASN cc_start: 0.8241 (t0) cc_final: 0.8006 (t0) REVERT: B 62 GLU cc_start: 0.7447 (mp0) cc_final: 0.7047 (mp0) REVERT: B 93 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.6878 (mtm-85) REVERT: B 133 MET cc_start: 0.7751 (mtp) cc_final: 0.7156 (tmm) REVERT: B 282 MET cc_start: 0.8156 (tpt) cc_final: 0.7747 (tpp) REVERT: B 391 MET cc_start: 0.6966 (mmt) cc_final: 0.6543 (mmm) REVERT: B 567 MET cc_start: 0.6993 (tpp) cc_final: 0.6718 (tpp) REVERT: C 114 GLU cc_start: 0.7786 (mp0) cc_final: 0.7532 (pm20) REVERT: C 183 MET cc_start: 0.8651 (mtt) cc_final: 0.8343 (mtp) REVERT: C 282 MET cc_start: 0.7625 (tpt) cc_final: 0.6929 (tpt) REVERT: C 520 LEU cc_start: 0.8463 (mt) cc_final: 0.7907 (tt) REVERT: D 142 ASN cc_start: 0.8240 (m110) cc_final: 0.7891 (m110) REVERT: D 190 VAL cc_start: 0.8279 (t) cc_final: 0.8034 (p) REVERT: D 194 MET cc_start: 0.7394 (mtp) cc_final: 0.7121 (mtp) REVERT: D 260 MET cc_start: 0.8986 (mmm) cc_final: 0.8521 (mmt) REVERT: D 276 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6842 (pt0) REVERT: D 296 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7415 (mm-30) REVERT: E 214 LEU cc_start: 0.7407 (mt) cc_final: 0.7139 (mt) REVERT: E 316 MET cc_start: 0.8632 (mtp) cc_final: 0.8042 (mtm) REVERT: E 411 TYR cc_start: 0.6184 (m-80) cc_final: 0.5921 (m-10) REVERT: F 11 ILE cc_start: 0.8753 (mm) cc_final: 0.8475 (mp) REVERT: F 88 MET cc_start: 0.7412 (ptm) cc_final: 0.6933 (ptm) REVERT: F 89 LEU cc_start: 0.8442 (mt) cc_final: 0.8090 (tp) REVERT: F 194 MET cc_start: 0.8178 (mpp) cc_final: 0.7749 (mmm) REVERT: F 287 MET cc_start: 0.6938 (ttm) cc_final: 0.6636 (ttm) REVERT: F 316 MET cc_start: 0.8593 (mtm) cc_final: 0.8254 (mtp) REVERT: G 144 GLU cc_start: 0.8397 (tt0) cc_final: 0.7738 (tm-30) REVERT: H 79 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6824 (mt-10) REVERT: J 78 GLU cc_start: 0.7466 (tp30) cc_final: 0.7169 (mt-10) REVERT: J 126 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7288 (mp0) REVERT: K 104 MET cc_start: 0.4563 (mpp) cc_final: 0.4277 (mpp) REVERT: L 84 ARG cc_start: 0.6026 (ttt90) cc_final: 0.5280 (ttp80) REVERT: L 110 GLU cc_start: 0.6200 (pt0) cc_final: 0.5063 (tt0) REVERT: L 172 ASP cc_start: 0.7686 (m-30) cc_final: 0.6935 (p0) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1852 time to fit residues: 87.1843 Evaluate side-chains 203 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 169 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 302 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN C 316 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.050973 restraints weight = 118441.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.052058 restraints weight = 76578.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.052815 restraints weight = 54270.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.053352 restraints weight = 41689.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.053733 restraints weight = 34369.071| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30015 Z= 0.173 Angle : 0.606 11.114 40658 Z= 0.308 Chirality : 0.045 0.170 4560 Planarity : 0.005 0.053 5330 Dihedral : 4.492 27.604 4180 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3764 helix: 1.08 (0.13), residues: 1564 sheet: -0.54 (0.23), residues: 543 loop : -0.93 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 88 TYR 0.014 0.001 TYR F 349 PHE 0.020 0.002 PHE G 40 TRP 0.036 0.001 TRP J 100 HIS 0.006 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00401 (30015) covalent geometry : angle 0.60574 (40658) hydrogen bonds : bond 0.04245 ( 1244) hydrogen bonds : angle 4.75100 ( 3594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 175 LEU cc_start: 0.7943 (mm) cc_final: 0.7343 (tp) REVERT: A 220 MET cc_start: 0.7982 (tpp) cc_final: 0.7514 (ttp) REVERT: A 336 GLU cc_start: 0.7457 (tp30) cc_final: 0.7024 (tp30) REVERT: A 391 MET cc_start: 0.7940 (mmm) cc_final: 0.7535 (tpp) REVERT: A 498 ASN cc_start: 0.8209 (t0) cc_final: 0.7983 (t0) REVERT: B 62 GLU cc_start: 0.7285 (mp0) cc_final: 0.6802 (mp0) REVERT: B 93 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.6824 (mtm-85) REVERT: B 133 MET cc_start: 0.7773 (mtp) cc_final: 0.7166 (tmm) REVERT: C 114 GLU cc_start: 0.7943 (mp0) cc_final: 0.7651 (pm20) REVERT: C 183 MET cc_start: 0.8583 (mtt) cc_final: 0.8270 (mtp) REVERT: C 282 MET cc_start: 0.7550 (tpt) cc_final: 0.6921 (tpt) REVERT: C 520 LEU cc_start: 0.8481 (mt) cc_final: 0.7945 (tt) REVERT: C 556 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7390 (tp30) REVERT: D 194 MET cc_start: 0.7428 (mtp) cc_final: 0.7176 (mtp) REVERT: D 260 MET cc_start: 0.8926 (mmm) cc_final: 0.8270 (mmm) REVERT: D 276 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6797 (pt0) REVERT: D 296 GLU cc_start: 0.7787 (mm-30) cc_final: 0.6883 (tp30) REVERT: E 194 MET cc_start: 0.8267 (mtm) cc_final: 0.7954 (pmm) REVERT: E 316 MET cc_start: 0.8680 (mtp) cc_final: 0.8020 (mtm) REVERT: E 411 TYR cc_start: 0.6167 (m-80) cc_final: 0.5872 (m-10) REVERT: F 88 MET cc_start: 0.7386 (ptm) cc_final: 0.6916 (ptm) REVERT: F 89 LEU cc_start: 0.8408 (mt) cc_final: 0.7985 (tp) REVERT: F 141 MET cc_start: 0.8602 (mtp) cc_final: 0.8380 (mtp) REVERT: F 194 MET cc_start: 0.8187 (mpp) cc_final: 0.7773 (mmm) REVERT: G 144 GLU cc_start: 0.8386 (tt0) cc_final: 0.7807 (tm-30) REVERT: J 78 GLU cc_start: 0.7464 (tp30) cc_final: 0.7103 (mt-10) REVERT: J 99 GLU cc_start: 0.6816 (pp20) cc_final: 0.6548 (pm20) REVERT: J 126 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7261 (mp0) REVERT: J 165 ASN cc_start: 0.6283 (p0) cc_final: 0.6024 (p0) REVERT: L 84 ARG cc_start: 0.6225 (ttt90) cc_final: 0.5595 (ttp80) REVERT: L 110 GLU cc_start: 0.6123 (pt0) cc_final: 0.5061 (tt0) REVERT: L 172 ASP cc_start: 0.7556 (m-30) cc_final: 0.6594 (p0) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1822 time to fit residues: 80.8251 Evaluate side-chains 206 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 85 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 356 optimal weight: 20.0000 chunk 369 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 328 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 318 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 365 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS L 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.050794 restraints weight = 118114.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.051861 restraints weight = 75804.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.052598 restraints weight = 53745.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.053141 restraints weight = 41560.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.053517 restraints weight = 34167.985| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30015 Z= 0.200 Angle : 0.637 11.757 40658 Z= 0.323 Chirality : 0.046 0.201 4560 Planarity : 0.005 0.049 5330 Dihedral : 4.593 20.419 4180 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3764 helix: 1.00 (0.13), residues: 1560 sheet: -0.67 (0.22), residues: 547 loop : -0.99 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 87 TYR 0.028 0.002 TYR A 500 PHE 0.022 0.002 PHE E 187 TRP 0.024 0.001 TRP A 330 HIS 0.005 0.001 HIS J 130 Details of bonding type rmsd covalent geometry : bond 0.00464 (30015) covalent geometry : angle 0.63681 (40658) hydrogen bonds : bond 0.04435 ( 1244) hydrogen bonds : angle 4.80162 ( 3594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.133 Fit side-chains REVERT: A 19 MET cc_start: 0.7732 (mmm) cc_final: 0.7210 (mmm) REVERT: A 133 MET cc_start: 0.7347 (mtt) cc_final: 0.6583 (mmt) REVERT: A 175 LEU cc_start: 0.7938 (mm) cc_final: 0.7335 (tp) REVERT: A 220 MET cc_start: 0.7964 (tpp) cc_final: 0.7493 (ttp) REVERT: A 336 GLU cc_start: 0.7289 (tp30) cc_final: 0.6945 (tp30) REVERT: A 391 MET cc_start: 0.7855 (mmm) cc_final: 0.7541 (tpp) REVERT: B 62 GLU cc_start: 0.7268 (mp0) cc_final: 0.6787 (mp0) REVERT: B 93 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.6739 (mtm-85) REVERT: B 133 MET cc_start: 0.7826 (mtp) cc_final: 0.6631 (tmm) REVERT: B 262 MET cc_start: 0.8538 (pmm) cc_final: 0.8205 (pmm) REVERT: B 391 MET cc_start: 0.6772 (mmt) cc_final: 0.6196 (mmm) REVERT: C 114 GLU cc_start: 0.8056 (mp0) cc_final: 0.7649 (pm20) REVERT: C 183 MET cc_start: 0.8526 (mtt) cc_final: 0.8219 (mtp) REVERT: C 282 MET cc_start: 0.7544 (tpt) cc_final: 0.6908 (tpt) REVERT: C 556 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7559 (tp30) REVERT: D 142 ASN cc_start: 0.8538 (m110) cc_final: 0.8288 (m110) REVERT: D 194 MET cc_start: 0.7368 (mtp) cc_final: 0.7113 (mtp) REVERT: D 260 MET cc_start: 0.8917 (mmm) cc_final: 0.8508 (tpp) REVERT: D 276 GLU cc_start: 0.7730 (mt-10) cc_final: 0.6743 (pt0) REVERT: D 296 GLU cc_start: 0.7817 (mm-30) cc_final: 0.6898 (tp30) REVERT: E 316 MET cc_start: 0.8778 (mtp) cc_final: 0.8019 (mtm) REVERT: E 411 TYR cc_start: 0.6140 (m-80) cc_final: 0.5916 (m-10) REVERT: F 88 MET cc_start: 0.7369 (ptm) cc_final: 0.6925 (ptm) REVERT: F 89 LEU cc_start: 0.8378 (mt) cc_final: 0.7982 (tp) REVERT: F 194 MET cc_start: 0.8207 (mpp) cc_final: 0.7417 (mmm) REVERT: F 287 MET cc_start: 0.6650 (ttm) cc_final: 0.6444 (ttm) REVERT: F 316 MET cc_start: 0.8632 (mtm) cc_final: 0.8323 (mtp) REVERT: G 144 GLU cc_start: 0.8365 (tt0) cc_final: 0.7805 (tm-30) REVERT: J 78 GLU cc_start: 0.7472 (tp30) cc_final: 0.7103 (mt-10) REVERT: J 126 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7295 (mp0) REVERT: J 165 ASN cc_start: 0.5999 (p0) cc_final: 0.5668 (p0) REVERT: L 84 ARG cc_start: 0.6169 (ttt90) cc_final: 0.5452 (ttp80) REVERT: L 110 GLU cc_start: 0.6206 (pt0) cc_final: 0.5092 (tt0) REVERT: L 172 ASP cc_start: 0.7588 (m-30) cc_final: 0.6506 (p0) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1794 time to fit residues: 77.8976 Evaluate side-chains 199 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 227 optimal weight: 0.0570 chunk 238 optimal weight: 10.0000 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN C 316 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.062225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.050967 restraints weight = 118484.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.052026 restraints weight = 76314.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.052777 restraints weight = 54266.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053309 restraints weight = 41923.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.053659 restraints weight = 34602.008| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30015 Z= 0.172 Angle : 0.613 11.266 40658 Z= 0.310 Chirality : 0.046 0.259 4560 Planarity : 0.005 0.050 5330 Dihedral : 4.548 25.899 4180 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3764 helix: 1.09 (0.13), residues: 1561 sheet: -0.62 (0.22), residues: 562 loop : -1.01 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 88 TYR 0.029 0.001 TYR C 166 PHE 0.029 0.002 PHE A 269 TRP 0.037 0.001 TRP J 100 HIS 0.006 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00401 (30015) covalent geometry : angle 0.61321 (40658) hydrogen bonds : bond 0.04262 ( 1244) hydrogen bonds : angle 4.75851 ( 3594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 175 LEU cc_start: 0.7858 (mm) cc_final: 0.7323 (tp) REVERT: A 220 MET cc_start: 0.7941 (tpp) cc_final: 0.7449 (ttp) REVERT: A 336 GLU cc_start: 0.7270 (tp30) cc_final: 0.6946 (tp30) REVERT: A 391 MET cc_start: 0.7836 (mmm) cc_final: 0.7523 (tpp) REVERT: B 62 GLU cc_start: 0.7234 (mp0) cc_final: 0.6748 (mp0) REVERT: B 93 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.6842 (mtm-85) REVERT: B 133 MET cc_start: 0.7877 (mtp) cc_final: 0.6592 (tmm) REVERT: B 567 MET cc_start: 0.6992 (tpp) cc_final: 0.6756 (tpp) REVERT: C 114 GLU cc_start: 0.8027 (mp0) cc_final: 0.7603 (pm20) REVERT: C 183 MET cc_start: 0.8564 (mtt) cc_final: 0.8209 (mtp) REVERT: C 282 MET cc_start: 0.7550 (tpt) cc_final: 0.6925 (tpt) REVERT: C 556 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7575 (tp30) REVERT: D 142 ASN cc_start: 0.8363 (m110) cc_final: 0.7385 (m110) REVERT: D 276 GLU cc_start: 0.7720 (mt-10) cc_final: 0.6723 (pt0) REVERT: D 296 GLU cc_start: 0.7747 (mm-30) cc_final: 0.6898 (tp30) REVERT: D 357 SER cc_start: 0.7855 (m) cc_final: 0.7639 (t) REVERT: D 407 ASN cc_start: 0.7292 (m-40) cc_final: 0.7091 (m-40) REVERT: E 237 MET cc_start: 0.7821 (mmm) cc_final: 0.7234 (mmt) REVERT: E 316 MET cc_start: 0.8761 (mtp) cc_final: 0.8027 (mtm) REVERT: E 411 TYR cc_start: 0.6194 (m-80) cc_final: 0.5938 (m-10) REVERT: F 88 MET cc_start: 0.7270 (ptm) cc_final: 0.6835 (ptm) REVERT: F 89 LEU cc_start: 0.8388 (mt) cc_final: 0.7997 (tp) REVERT: F 194 MET cc_start: 0.8242 (mpp) cc_final: 0.7502 (mmm) REVERT: F 316 MET cc_start: 0.8619 (mtm) cc_final: 0.8342 (mtp) REVERT: G 144 GLU cc_start: 0.8352 (tt0) cc_final: 0.7806 (tm-30) REVERT: I 106 ARG cc_start: 0.5927 (mmt180) cc_final: 0.5478 (mpt180) REVERT: J 78 GLU cc_start: 0.7448 (tp30) cc_final: 0.7072 (mt-10) REVERT: J 126 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7321 (mp0) REVERT: J 165 ASN cc_start: 0.5797 (p0) cc_final: 0.5592 (p0) REVERT: L 84 ARG cc_start: 0.6143 (ttt90) cc_final: 0.5509 (ttp80) REVERT: L 110 GLU cc_start: 0.6193 (pt0) cc_final: 0.5072 (tt0) REVERT: L 172 ASP cc_start: 0.7538 (m-30) cc_final: 0.6503 (p0) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1845 time to fit residues: 79.0814 Evaluate side-chains 207 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 144 optimal weight: 3.9990 chunk 322 optimal weight: 0.0270 chunk 13 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 362 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 303 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 317 optimal weight: 7.9990 chunk 366 optimal weight: 7.9990 overall best weight: 3.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.051147 restraints weight = 119453.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.052218 restraints weight = 76946.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.052984 restraints weight = 54837.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.053521 restraints weight = 42374.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.053856 restraints weight = 35057.948| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30015 Z= 0.164 Angle : 0.611 12.430 40658 Z= 0.308 Chirality : 0.046 0.250 4560 Planarity : 0.005 0.051 5330 Dihedral : 4.499 20.726 4180 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -0.11 (0.14), residues: 3764 helix: 1.12 (0.13), residues: 1562 sheet: -0.60 (0.22), residues: 562 loop : -1.00 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 138 TYR 0.018 0.001 TYR A 500 PHE 0.028 0.002 PHE A 269 TRP 0.036 0.001 TRP J 187 HIS 0.006 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00382 (30015) covalent geometry : angle 0.61081 (40658) hydrogen bonds : bond 0.04161 ( 1244) hydrogen bonds : angle 4.73789 ( 3594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.055 Fit side-chains REVERT: A 19 MET cc_start: 0.7651 (mmm) cc_final: 0.7211 (mmm) REVERT: A 24 MET cc_start: 0.8348 (tpp) cc_final: 0.7849 (tpp) REVERT: A 175 LEU cc_start: 0.7890 (mm) cc_final: 0.7246 (tp) REVERT: A 220 MET cc_start: 0.7999 (tpp) cc_final: 0.7556 (ttp) REVERT: A 336 GLU cc_start: 0.7277 (tp30) cc_final: 0.6990 (tp30) REVERT: B 62 GLU cc_start: 0.7175 (mp0) cc_final: 0.6676 (mp0) REVERT: B 93 ARG cc_start: 0.7508 (mtm-85) cc_final: 0.6880 (mtm-85) REVERT: B 133 MET cc_start: 0.7901 (mtp) cc_final: 0.6599 (tmm) REVERT: B 262 MET cc_start: 0.8676 (pmm) cc_final: 0.7964 (pmm) REVERT: B 282 MET cc_start: 0.8458 (mmm) cc_final: 0.8215 (mmm) REVERT: B 391 MET cc_start: 0.6793 (mmt) cc_final: 0.6305 (mmm) REVERT: B 567 MET cc_start: 0.6950 (tpp) cc_final: 0.6740 (tpp) REVERT: C 114 GLU cc_start: 0.8062 (mp0) cc_final: 0.7651 (pm20) REVERT: C 183 MET cc_start: 0.8584 (mtt) cc_final: 0.8233 (mtp) REVERT: C 282 MET cc_start: 0.7563 (tpt) cc_final: 0.6935 (tpt) REVERT: C 556 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7586 (tp30) REVERT: D 142 ASN cc_start: 0.8428 (m110) cc_final: 0.7511 (m110) REVERT: D 276 GLU cc_start: 0.7972 (mt-10) cc_final: 0.6770 (pt0) REVERT: D 296 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7082 (mm-30) REVERT: E 316 MET cc_start: 0.8719 (mtp) cc_final: 0.8082 (mtm) REVERT: E 411 TYR cc_start: 0.6167 (m-80) cc_final: 0.5926 (m-10) REVERT: F 39 THR cc_start: 0.7905 (m) cc_final: 0.7685 (m) REVERT: F 88 MET cc_start: 0.7231 (ptm) cc_final: 0.6805 (ptm) REVERT: F 89 LEU cc_start: 0.8401 (mt) cc_final: 0.8001 (tp) REVERT: F 194 MET cc_start: 0.8264 (mpp) cc_final: 0.7465 (mmm) REVERT: F 287 MET cc_start: 0.6545 (ttm) cc_final: 0.6319 (ttm) REVERT: F 316 MET cc_start: 0.8642 (mtm) cc_final: 0.8302 (mtp) REVERT: G 144 GLU cc_start: 0.8336 (tt0) cc_final: 0.7775 (tm-30) REVERT: I 106 ARG cc_start: 0.5969 (mmt180) cc_final: 0.5353 (mtp180) REVERT: J 78 GLU cc_start: 0.7469 (tp30) cc_final: 0.7085 (mt-10) REVERT: J 126 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7319 (mp0) REVERT: L 84 ARG cc_start: 0.6150 (ttt90) cc_final: 0.5479 (ttp80) REVERT: L 88 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7414 (ttp80) REVERT: L 110 GLU cc_start: 0.6254 (pt0) cc_final: 0.4975 (tt0) REVERT: L 172 ASP cc_start: 0.7422 (m-30) cc_final: 0.6376 (p0) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1765 time to fit residues: 74.9981 Evaluate side-chains 196 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 147 optimal weight: 0.8980 chunk 281 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 363 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 186 optimal weight: 0.1980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051033 restraints weight = 119105.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.052097 restraints weight = 76922.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.052843 restraints weight = 55049.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.053378 restraints weight = 42654.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.053744 restraints weight = 35305.510| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30015 Z= 0.173 Angle : 0.626 12.175 40658 Z= 0.316 Chirality : 0.046 0.246 4560 Planarity : 0.005 0.063 5330 Dihedral : 4.546 25.472 4180 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3764 helix: 1.11 (0.13), residues: 1562 sheet: -0.70 (0.22), residues: 546 loop : -1.05 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 91 TYR 0.016 0.001 TYR D 331 PHE 0.027 0.002 PHE A 269 TRP 0.024 0.001 TRP J 100 HIS 0.006 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00402 (30015) covalent geometry : angle 0.62637 (40658) hydrogen bonds : bond 0.04242 ( 1244) hydrogen bonds : angle 4.77844 ( 3594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.7899 (mm) cc_final: 0.7242 (tp) REVERT: A 220 MET cc_start: 0.7961 (tpp) cc_final: 0.7552 (ttp) REVERT: A 336 GLU cc_start: 0.7321 (tp30) cc_final: 0.7028 (tp30) REVERT: B 93 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.6897 (mtm-85) REVERT: B 133 MET cc_start: 0.7829 (mtp) cc_final: 0.6593 (tmm) REVERT: B 262 MET cc_start: 0.8630 (pmm) cc_final: 0.7897 (pmm) REVERT: B 282 MET cc_start: 0.8455 (mmm) cc_final: 0.8229 (mmm) REVERT: B 391 MET cc_start: 0.6826 (mmt) cc_final: 0.6294 (mmm) REVERT: B 567 MET cc_start: 0.6933 (tpp) cc_final: 0.6698 (tpp) REVERT: C 114 GLU cc_start: 0.8052 (mp0) cc_final: 0.7632 (pm20) REVERT: C 183 MET cc_start: 0.8577 (mtt) cc_final: 0.8224 (mtp) REVERT: C 282 MET cc_start: 0.7580 (tpt) cc_final: 0.6948 (tpt) REVERT: C 509 MET cc_start: 0.8373 (mmp) cc_final: 0.8063 (mmt) REVERT: C 556 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7682 (tp30) REVERT: D 276 GLU cc_start: 0.7900 (mt-10) cc_final: 0.6784 (pt0) REVERT: D 296 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7129 (mm-30) REVERT: E 237 MET cc_start: 0.7842 (mmm) cc_final: 0.7243 (mmt) REVERT: E 316 MET cc_start: 0.8727 (mtp) cc_final: 0.8038 (mtm) REVERT: E 411 TYR cc_start: 0.6195 (m-80) cc_final: 0.5951 (m-10) REVERT: F 39 THR cc_start: 0.7867 (m) cc_final: 0.7647 (m) REVERT: F 88 MET cc_start: 0.7205 (ptm) cc_final: 0.6758 (ptm) REVERT: F 89 LEU cc_start: 0.8419 (mt) cc_final: 0.8011 (tp) REVERT: F 194 MET cc_start: 0.8247 (mpp) cc_final: 0.7845 (mmm) REVERT: F 316 MET cc_start: 0.8643 (mtm) cc_final: 0.8343 (mtp) REVERT: G 144 GLU cc_start: 0.8321 (tt0) cc_final: 0.7747 (tm-30) REVERT: G 153 GLU cc_start: 0.7491 (tp30) cc_final: 0.7159 (tp30) REVERT: I 106 ARG cc_start: 0.6024 (mmt180) cc_final: 0.5419 (mtp180) REVERT: J 78 GLU cc_start: 0.7465 (tp30) cc_final: 0.7090 (mt-10) REVERT: J 126 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7227 (mp0) REVERT: L 74 GLN cc_start: 0.7037 (pt0) cc_final: 0.6698 (pp30) REVERT: L 84 ARG cc_start: 0.6150 (ttt90) cc_final: 0.5619 (ttp80) REVERT: L 88 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7394 (ttp80) REVERT: L 110 GLU cc_start: 0.6159 (pt0) cc_final: 0.5076 (tt0) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1855 time to fit residues: 76.4175 Evaluate side-chains 196 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 330 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 65 optimal weight: 0.0770 chunk 146 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 348 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.051743 restraints weight = 117959.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.052845 restraints weight = 75872.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.053620 restraints weight = 53654.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054161 restraints weight = 41229.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.054504 restraints weight = 33925.417| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30015 Z= 0.136 Angle : 0.593 12.002 40658 Z= 0.299 Chirality : 0.045 0.241 4560 Planarity : 0.004 0.049 5330 Dihedral : 4.402 21.591 4180 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3764 helix: 1.20 (0.14), residues: 1566 sheet: -0.65 (0.22), residues: 544 loop : -0.98 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 88 TYR 0.023 0.001 TYR E 349 PHE 0.026 0.001 PHE A 269 TRP 0.024 0.001 TRP A 330 HIS 0.005 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00313 (30015) covalent geometry : angle 0.59284 (40658) hydrogen bonds : bond 0.03934 ( 1244) hydrogen bonds : angle 4.67256 ( 3594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3812.68 seconds wall clock time: 67 minutes 12.94 seconds (4032.94 seconds total)