Starting phenix.real_space_refine on Thu Feb 5 22:17:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vl4_65154/02_2026/9vl4_65154.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vl4_65154/02_2026/9vl4_65154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vl4_65154/02_2026/9vl4_65154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vl4_65154/02_2026/9vl4_65154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vl4_65154/02_2026/9vl4_65154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vl4_65154/02_2026/9vl4_65154.map" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.704 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 108 5.16 5 C 13062 2.51 5 N 3438 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20508 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "D" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "E" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "F" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Time building chain proxies: 5.22, per 1000 atoms: 0.25 Number of scatterers: 20508 At special positions: 0 Unit cell: (182.24, 179.52, 84.32, 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 108 16.00 O 3900 8.00 N 3438 7.00 C 13062 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: 1.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4908 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 40 sheets defined 21.9% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 345 through 373 removed outlier: 3.513A pdb=" N LEU B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 removed outlier: 3.924A pdb=" N TRP B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 536 through 539 Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 345 through 373 removed outlier: 3.659A pdb=" N LEU C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 removed outlier: 3.898A pdb=" N TRP C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 431 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.923A pdb=" N ALA D 155 " --> pdb=" O THR D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 332 through 343 Processing helix chain 'D' and resid 345 through 373 removed outlier: 3.687A pdb=" N SER D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 removed outlier: 3.769A pdb=" N TRP D 393 " --> pdb=" O SER D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 432 removed outlier: 3.585A pdb=" N GLN D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 476 Processing helix chain 'D' and resid 536 through 539 Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.855A pdb=" N ALA E 155 " --> pdb=" O THR E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 332 through 343 Processing helix chain 'E' and resid 345 through 374 removed outlier: 3.812A pdb=" N SER E 359 " --> pdb=" O LYS E 355 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 367 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR E 374 " --> pdb=" O MET E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 413 removed outlier: 3.673A pdb=" N TRP E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.552A pdb=" N GLN E 432 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 476 Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'F' and resid 220 through 224 Processing helix chain 'F' and resid 332 through 342 Processing helix chain 'F' and resid 345 through 373 removed outlier: 3.826A pdb=" N SER F 359 " --> pdb=" O LYS F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 413 removed outlier: 3.899A pdb=" N TRP F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 431 Processing helix chain 'F' and resid 466 through 475 Processing helix chain 'F' and resid 537 through 539 No H-bonds generated for 'chain 'F' and resid 537 through 539' Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.572A pdb=" N ALA A 155 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 345 through 374 removed outlier: 3.751A pdb=" N SER A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 removed outlier: 3.792A pdb=" N TRP A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 432 removed outlier: 3.547A pdb=" N GLN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 536 through 539 Processing sheet with id=AA1, first strand: chain 'B' and resid 141 through 143 removed outlier: 4.142A pdb=" N ALA B 141 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 169 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 166 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 170 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 157 through 158 removed outlier: 5.549A pdb=" N THR B 157 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP B 503 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY B 502 " --> pdb=" O ASP B 531 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASP B 531 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 504 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE B 529 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER B 527 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP B 525 " --> pdb=" O ILE B 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 310 through 314 removed outlier: 7.861A pdb=" N TYR B 169 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET C 142 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL B 171 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 200 through 206 removed outlier: 6.571A pdb=" N ILE B 292 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 215 through 219 Processing sheet with id=AA6, first strand: chain 'B' and resid 377 through 381 removed outlier: 6.562A pdb=" N ASP B 378 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 547 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE B 380 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 488 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 461 " --> pdb=" O MET B 418 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY B 454 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU B 464 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TYR B 452 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 384 through 385 removed outlier: 3.924A pdb=" N LEU B 384 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 157 through 158 removed outlier: 5.943A pdb=" N THR C 157 " --> pdb=" O THR C 501 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASP C 503 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY C 502 " --> pdb=" O ASP C 531 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP C 531 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA C 504 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE C 529 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER C 527 " --> pdb=" O PRO C 506 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP C 525 " --> pdb=" O ILE C 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 310 through 319 removed outlier: 3.642A pdb=" N GLU C 313 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 170 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 166 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 200 through 206 removed outlier: 6.584A pdb=" N ILE C 292 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 215 through 219 Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 381 removed outlier: 6.434A pdb=" N ALA C 376 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N THR C 545 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP C 378 " --> pdb=" O THR C 545 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR C 547 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE C 380 " --> pdb=" O THR C 547 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY C 454 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU C 464 " --> pdb=" O TYR C 452 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR C 452 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 384 through 385 removed outlier: 3.800A pdb=" N LEU C 384 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 157 through 158 removed outlier: 5.892A pdb=" N THR D 157 " --> pdb=" O THR D 501 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASP D 503 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLY D 502 " --> pdb=" O ASP D 531 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ASP D 531 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA D 504 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ILE D 529 " --> pdb=" O ALA D 504 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER D 527 " --> pdb=" O PRO D 506 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG D 521 " --> pdb=" O HIS D 512 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 522 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 310 through 314 removed outlier: 3.688A pdb=" N GLU D 313 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 172 " --> pdb=" O GLU D 313 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER D 166 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 310 through 314 removed outlier: 3.688A pdb=" N GLU D 313 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 172 " --> pdb=" O GLU D 313 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP D 167 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N MET E 142 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR D 169 " --> pdb=" O MET E 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 200 through 206 removed outlier: 6.704A pdb=" N ILE D 292 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 215 through 219 removed outlier: 3.749A pdb=" N LEU D 253 " --> pdb=" O CYS D 269 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 377 through 381 removed outlier: 6.381A pdb=" N ASP D 378 " --> pdb=" O THR D 545 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR D 547 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE D 380 " --> pdb=" O THR D 547 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR D 488 " --> pdb=" O GLY D 419 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS D 461 " --> pdb=" O MET D 418 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY D 454 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU D 464 " --> pdb=" O TYR D 452 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR D 452 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 384 through 385 removed outlier: 3.896A pdb=" N LEU D 384 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 157 through 158 removed outlier: 5.126A pdb=" N THR E 501 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASP E 531 " --> pdb=" O THR E 501 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP E 503 " --> pdb=" O ILE E 529 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE E 529 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA E 507 " --> pdb=" O TRP E 525 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TRP E 525 " --> pdb=" O ALA E 507 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR E 523 " --> pdb=" O PRO E 509 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN E 511 " --> pdb=" O ARG E 521 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ARG E 521 " --> pdb=" O GLN E 511 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 310 through 316 removed outlier: 3.756A pdb=" N GLU E 313 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 170 " --> pdb=" O LYS E 315 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP E 167 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N MET F 142 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR E 169 " --> pdb=" O MET F 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 200 through 206 removed outlier: 6.823A pdb=" N ILE E 292 " --> pdb=" O LEU E 205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 215 through 219 Processing sheet with id=AC7, first strand: chain 'E' and resid 215 through 219 removed outlier: 3.585A pdb=" N GLN E 277 " --> pdb=" O ASN E 272 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 377 through 381 removed outlier: 6.738A pdb=" N ASP E 378 " --> pdb=" O THR E 545 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N THR E 547 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE E 380 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR E 488 " --> pdb=" O GLY E 419 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY E 454 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU E 464 " --> pdb=" O TYR E 452 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR E 452 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 384 through 385 removed outlier: 3.740A pdb=" N LEU E 384 " --> pdb=" O LEU E 554 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 157 through 158 removed outlier: 5.929A pdb=" N THR F 157 " --> pdb=" O THR F 501 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASP F 503 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR F 501 " --> pdb=" O ASP F 531 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ASP F 531 " --> pdb=" O THR F 501 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASP F 503 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE F 529 " --> pdb=" O ASP F 503 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA F 507 " --> pdb=" O TRP F 525 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP F 525 " --> pdb=" O ALA F 507 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR F 523 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLN F 511 " --> pdb=" O ARG F 521 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ARG F 521 " --> pdb=" O GLN F 511 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 314 through 319 removed outlier: 3.698A pdb=" N GLU F 170 " --> pdb=" O LYS F 315 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER F 166 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR F 169 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET A 142 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL F 171 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AD4, first strand: chain 'F' and resid 200 through 206 removed outlier: 6.856A pdb=" N ILE F 292 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 215 through 219 Processing sheet with id=AD6, first strand: chain 'F' and resid 376 through 381 removed outlier: 6.482A pdb=" N ALA F 376 " --> pdb=" O ARG F 543 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR F 545 " --> pdb=" O ALA F 376 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP F 378 " --> pdb=" O THR F 545 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR F 547 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE F 380 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY F 454 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU F 464 " --> pdb=" O TYR F 452 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR F 452 " --> pdb=" O GLU F 464 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 384 through 385 removed outlier: 3.838A pdb=" N LEU F 384 " --> pdb=" O LEU F 554 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN F 555 " --> pdb=" O ASP F 560 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP F 560 " --> pdb=" O ASN F 555 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 157 through 158 removed outlier: 5.612A pdb=" N THR A 157 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP A 503 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY A 502 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP A 531 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA A 504 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE A 529 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER A 527 " --> pdb=" O PRO A 506 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG A 521 " --> pdb=" O HIS A 512 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 520 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AE1, first strand: chain 'A' and resid 200 through 206 removed outlier: 6.643A pdb=" N ILE A 292 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 215 through 219 removed outlier: 3.560A pdb=" N HIS A 255 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 377 through 381 removed outlier: 6.410A pdb=" N ASP A 378 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR A 547 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE A 380 " --> pdb=" O THR A 547 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 461 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY A 454 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU A 464 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR A 452 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 384 through 385 removed outlier: 3.912A pdb=" N LEU A 384 " --> pdb=" O LEU A 554 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2142 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: 3.44 Time building geometry restraints manager: 2.12 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: 6734 1.34 - 1.46: 4741 1.46 - 1.58: 9278 1.58 - 1.70: 1 1.70 - 1.82: 192 Bond restraints: 20946 Sorted by residual: bond pdb=" CB PRO A 516 " pdb=" CG PRO A 516 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.48e+00 bond pdb=" CA ILE A 508 " pdb=" C ILE A 508 " ideal model delta sigma weight residual 1.525 1.510 0.015 8.80e-03 1.29e+04 3.02e+00 bond pdb=" CB LYS B 435 " pdb=" CG LYS B 435 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CG LYS D 435 " pdb=" CD LYS D 435 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CB LYS D 435 " pdb=" CG LYS D 435 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 20941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 28009 1.89 - 3.78: 362 3.78 - 5.66: 41 5.66 - 7.55: 10 7.55 - 9.44: 6 Bond angle restraints: 28428 Sorted by residual: angle pdb=" CA PRO A 516 " pdb=" N PRO A 516 " pdb=" CD PRO A 516 " ideal model delta sigma weight residual 112.00 105.54 6.46 1.40e+00 5.10e-01 2.13e+01 angle pdb=" N ILE A 275 " pdb=" CA ILE A 275 " pdb=" C ILE A 275 " ideal model delta sigma weight residual 113.53 109.37 4.16 9.80e-01 1.04e+00 1.80e+01 angle pdb=" CA LYS B 435 " pdb=" CB LYS B 435 " pdb=" CG LYS B 435 " ideal model delta sigma weight residual 114.10 122.25 -8.15 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CB LYS D 435 " pdb=" CG LYS D 435 " pdb=" CD LYS D 435 " ideal model delta sigma weight residual 111.30 120.64 -9.34 2.30e+00 1.89e-01 1.65e+01 angle pdb=" C MET D 134 " pdb=" N ARG D 135 " pdb=" CA ARG D 135 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 ... (remaining 28423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11130 17.99 - 35.98: 1112 35.98 - 53.97: 203 53.97 - 71.96: 25 71.96 - 89.94: 22 Dihedral angle restraints: 12492 sinusoidal: 4854 harmonic: 7638 Sorted by residual: dihedral pdb=" CA ASP B 539 " pdb=" CB ASP B 539 " pdb=" CG ASP B 539 " pdb=" OD1 ASP B 539 " ideal model delta sinusoidal sigma weight residual -30.00 -88.84 58.84 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP B 484 " pdb=" CB ASP B 484 " pdb=" CG ASP B 484 " pdb=" OD1 ASP B 484 " ideal model delta sinusoidal sigma weight residual -30.00 -88.41 58.41 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP D 539 " pdb=" CB ASP D 539 " pdb=" CG ASP D 539 " pdb=" OD1 ASP D 539 " ideal model delta sinusoidal sigma weight residual -30.00 -87.84 57.84 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 12489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2042 0.030 - 0.060: 724 0.060 - 0.089: 213 0.089 - 0.119: 205 0.119 - 0.149: 38 Chirality restraints: 3222 Sorted by residual: chirality pdb=" CA ASN A 536 " pdb=" N ASN A 536 " pdb=" C ASN A 536 " pdb=" CB ASN A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE E 326 " pdb=" N ILE E 326 " pdb=" C ILE E 326 " pdb=" CB ILE E 326 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CB VAL B 129 " pdb=" CA VAL B 129 " pdb=" CG1 VAL B 129 " pdb=" CG2 VAL B 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 3219 not shown) Planarity restraints: 3690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 515 " -0.081 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO A 516 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 136 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO E 137 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO E 137 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 137 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 303 " -0.042 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO F 304 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 304 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 304 " -0.036 5.00e-02 4.00e+02 ... (remaining 3687 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 508 2.69 - 3.24: 19508 3.24 - 3.79: 30416 3.79 - 4.35: 38911 4.35 - 4.90: 67086 Nonbonded interactions: 156429 Sorted by model distance: nonbonded pdb=" OG SER F 389 " pdb=" OD1 ASP F 391 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR D 157 " pdb=" O PHE D 499 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR E 405 " pdb=" O GLY E 419 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR E 152 " pdb=" OD1 ASP E 363 " model vdw 2.239 3.040 nonbonded pdb=" O VAL D 133 " pdb=" NH2 ARG D 135 " model vdw 2.243 3.120 ... (remaining 156424 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.700 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.360 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 20946 Z= 0.119 Angle : 0.557 9.439 28428 Z= 0.309 Chirality : 0.043 0.149 3222 Planarity : 0.005 0.120 3690 Dihedral : 14.629 89.944 7584 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.11 % Rotamer: Outliers : 0.09 % Allowed : 15.85 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.16), residues: 2628 helix: 1.85 (0.23), residues: 552 sheet: 0.35 (0.19), residues: 773 loop : -1.13 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 340 TYR 0.019 0.001 TYR B 444 PHE 0.015 0.001 PHE E 556 TRP 0.007 0.001 TRP C 393 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00241 (20946) covalent geometry : angle 0.55721 (28428) hydrogen bonds : bond 0.20699 ( 745) hydrogen bonds : angle 7.92110 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 418 MET cc_start: 0.8144 (mmt) cc_final: 0.7895 (mmt) REVERT: C 147 GLN cc_start: 0.7785 (tt0) cc_final: 0.7530 (pt0) REVERT: A 139 PHE cc_start: 0.7591 (t80) cc_final: 0.7382 (t80) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.1326 time to fit residues: 33.8518 Evaluate side-chains 148 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN D 432 GLN E 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.058462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.047167 restraints weight = 70847.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.048958 restraints weight = 32672.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.050148 restraints weight = 19283.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.050945 restraints weight = 13125.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.051471 restraints weight = 9863.847| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20946 Z= 0.183 Angle : 0.559 9.186 28428 Z= 0.300 Chirality : 0.045 0.154 3222 Planarity : 0.005 0.072 3690 Dihedral : 4.357 16.287 2850 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 2.66 % Allowed : 13.64 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2628 helix: 1.59 (0.22), residues: 568 sheet: 0.36 (0.18), residues: 767 loop : -1.19 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 340 TYR 0.016 0.002 TYR F 238 PHE 0.012 0.001 PHE B 401 TRP 0.003 0.001 TRP F 525 HIS 0.005 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00426 (20946) covalent geometry : angle 0.55910 (28428) hydrogen bonds : bond 0.05323 ( 745) hydrogen bonds : angle 5.47822 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: B 531 ASP cc_start: 0.8542 (t0) cc_final: 0.8340 (t70) REVERT: D 435 LYS cc_start: 0.8900 (tppt) cc_final: 0.8585 (tppt) REVERT: F 363 ASP cc_start: 0.8089 (t0) cc_final: 0.7727 (t0) REVERT: F 407 ASP cc_start: 0.9092 (m-30) cc_final: 0.8536 (m-30) REVERT: F 536 ASN cc_start: 0.8042 (t0) cc_final: 0.7603 (t0) REVERT: A 142 MET cc_start: 0.8997 (mmm) cc_final: 0.8726 (tpp) REVERT: A 290 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8329 (p) outliers start: 59 outliers final: 30 residues processed: 195 average time/residue: 0.1258 time to fit residues: 40.0719 Evaluate side-chains 163 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 113 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 GLN C 432 GLN A 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.055144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.044049 restraints weight = 72939.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.045801 restraints weight = 33293.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.046969 restraints weight = 19467.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.047754 restraints weight = 13210.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.048292 restraints weight = 9903.268| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 20946 Z= 0.270 Angle : 0.619 12.335 28428 Z= 0.333 Chirality : 0.046 0.166 3222 Planarity : 0.005 0.061 3690 Dihedral : 4.834 19.285 2850 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.08 % Rotamer: Outliers : 3.30 % Allowed : 15.00 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.16), residues: 2628 helix: 1.37 (0.22), residues: 563 sheet: 0.22 (0.18), residues: 774 loop : -1.30 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 340 TYR 0.015 0.002 TYR A 196 PHE 0.013 0.002 PHE B 401 TRP 0.005 0.001 TRP D 525 HIS 0.005 0.001 HIS D 360 Details of bonding type rmsd covalent geometry : bond 0.00628 (20946) covalent geometry : angle 0.61861 (28428) hydrogen bonds : bond 0.06200 ( 745) hydrogen bonds : angle 5.40836 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 135 time to evaluate : 0.764 Fit side-chains REVERT: B 337 GLU cc_start: 0.8740 (tt0) cc_final: 0.8399 (tm-30) REVERT: C 135 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.9010 (mmt90) REVERT: C 290 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8839 (p) REVERT: D 220 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8664 (mtp) REVERT: D 435 LYS cc_start: 0.9060 (tppt) cc_final: 0.8755 (tppt) REVERT: E 125 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: E 232 LYS cc_start: 0.9213 (mtmt) cc_final: 0.9001 (mttm) REVERT: E 390 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8310 (t80) REVERT: F 407 ASP cc_start: 0.9177 (m-30) cc_final: 0.8673 (m-30) REVERT: F 532 MET cc_start: 0.8778 (ttm) cc_final: 0.8499 (mtt) REVERT: F 536 ASN cc_start: 0.8217 (t0) cc_final: 0.7953 (t0) REVERT: F 548 MET cc_start: 0.9174 (tmm) cc_final: 0.8733 (tmm) REVERT: A 142 MET cc_start: 0.8508 (mmm) cc_final: 0.8134 (mmm) REVERT: A 165 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: A 220 MET cc_start: 0.8009 (ptm) cc_final: 0.7539 (ttp) outliers start: 73 outliers final: 38 residues processed: 191 average time/residue: 0.1289 time to fit residues: 40.2369 Evaluate side-chains 170 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 393 TRP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 496 LYS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 390 PHE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 519 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 75 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 GLN C 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.056916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.045813 restraints weight = 71074.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.047627 restraints weight = 32041.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.048826 restraints weight = 18635.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.049628 restraints weight = 12488.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.050157 restraints weight = 9315.970| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20946 Z= 0.135 Angle : 0.509 8.911 28428 Z= 0.272 Chirality : 0.044 0.148 3222 Planarity : 0.004 0.057 3690 Dihedral : 4.385 15.900 2850 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 3.12 % Allowed : 15.49 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.16), residues: 2628 helix: 1.52 (0.22), residues: 568 sheet: 0.22 (0.18), residues: 769 loop : -1.28 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 340 TYR 0.014 0.001 TYR B 444 PHE 0.011 0.001 PHE F 172 TRP 0.006 0.001 TRP F 525 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00308 (20946) covalent geometry : angle 0.50950 (28428) hydrogen bonds : bond 0.04755 ( 745) hydrogen bonds : angle 4.95453 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 133 time to evaluate : 0.830 Fit side-chains REVERT: B 126 MET cc_start: 0.8150 (mmm) cc_final: 0.7807 (mmm) REVERT: B 329 GLU cc_start: 0.7633 (tp30) cc_final: 0.7273 (tp30) REVERT: C 135 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.9069 (mmt90) REVERT: C 290 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8864 (p) REVERT: D 126 MET cc_start: 0.6566 (pmm) cc_final: 0.6232 (pmm) REVERT: D 220 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8589 (mtp) REVERT: D 435 LYS cc_start: 0.9044 (tppt) cc_final: 0.8692 (tppt) REVERT: E 232 LYS cc_start: 0.9193 (mtmt) cc_final: 0.8988 (mttm) REVERT: E 234 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8876 (mmt90) REVERT: E 390 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8281 (t80) REVERT: F 390 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8646 (t80) REVERT: F 407 ASP cc_start: 0.9136 (m-30) cc_final: 0.8587 (m-30) REVERT: F 532 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8363 (mtt) REVERT: F 536 ASN cc_start: 0.8195 (t0) cc_final: 0.7902 (t0) REVERT: A 142 MET cc_start: 0.8621 (mmm) cc_final: 0.8313 (mmm) REVERT: A 165 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: A 337 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8216 (tt0) outliers start: 69 outliers final: 38 residues processed: 190 average time/residue: 0.1400 time to fit residues: 42.7610 Evaluate side-chains 172 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 CYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 496 LYS Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 390 PHE Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 532 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 232 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 0.0470 chunk 161 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 432 GLN F 255 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.058164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.047188 restraints weight = 70586.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.048995 restraints weight = 32157.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.050183 restraints weight = 18824.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.050960 restraints weight = 12738.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.051517 restraints weight = 9550.262| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20946 Z= 0.104 Angle : 0.481 7.181 28428 Z= 0.255 Chirality : 0.043 0.143 3222 Planarity : 0.004 0.056 3690 Dihedral : 4.115 15.754 2850 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.94 % Allowed : 15.85 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.16), residues: 2628 helix: 1.60 (0.22), residues: 570 sheet: 0.24 (0.18), residues: 776 loop : -1.24 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 340 TYR 0.010 0.001 TYR F 238 PHE 0.012 0.001 PHE F 172 TRP 0.006 0.001 TRP F 525 HIS 0.004 0.000 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00228 (20946) covalent geometry : angle 0.48111 (28428) hydrogen bonds : bond 0.04098 ( 745) hydrogen bonds : angle 4.73477 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 139 time to evaluate : 0.841 Fit side-chains REVERT: B 126 MET cc_start: 0.8232 (mmm) cc_final: 0.7890 (mmm) REVERT: B 167 ASP cc_start: 0.8708 (m-30) cc_final: 0.8412 (m-30) REVERT: B 329 GLU cc_start: 0.7637 (tp30) cc_final: 0.7402 (tp30) REVERT: C 135 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8936 (mmt90) REVERT: C 290 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8905 (p) REVERT: D 435 LYS cc_start: 0.9052 (tppt) cc_final: 0.8555 (tppt) REVERT: E 125 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: E 390 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8250 (t80) REVERT: F 390 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8611 (t80) REVERT: F 536 ASN cc_start: 0.8124 (t0) cc_final: 0.7828 (t0) REVERT: A 142 MET cc_start: 0.8647 (mmm) cc_final: 0.8351 (mmm) REVERT: A 165 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: A 329 GLU cc_start: 0.8951 (tt0) cc_final: 0.8682 (tm-30) REVERT: A 337 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8334 (tt0) outliers start: 65 outliers final: 38 residues processed: 191 average time/residue: 0.1412 time to fit residues: 43.6011 Evaluate side-chains 177 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 269 CYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 496 LYS Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 390 PHE Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 532 MET Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 112 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 231 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 191 optimal weight: 0.0040 chunk 163 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 432 GLN F 312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.058177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.047158 restraints weight = 70677.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.048993 restraints weight = 31800.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.050204 restraints weight = 18378.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.051009 restraints weight = 12336.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.051556 restraints weight = 9157.735| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20946 Z= 0.108 Angle : 0.482 7.283 28428 Z= 0.254 Chirality : 0.043 0.143 3222 Planarity : 0.004 0.054 3690 Dihedral : 4.018 15.956 2850 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.76 % Allowed : 16.58 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.16), residues: 2628 helix: 1.83 (0.22), residues: 552 sheet: 0.19 (0.18), residues: 785 loop : -1.19 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 340 TYR 0.010 0.001 TYR F 238 PHE 0.012 0.001 PHE F 172 TRP 0.005 0.001 TRP F 525 HIS 0.004 0.000 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00241 (20946) covalent geometry : angle 0.48158 (28428) hydrogen bonds : bond 0.03995 ( 745) hydrogen bonds : angle 4.63834 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 134 time to evaluate : 0.585 Fit side-chains REVERT: B 126 MET cc_start: 0.8346 (mmm) cc_final: 0.8015 (mmm) REVERT: B 167 ASP cc_start: 0.8653 (m-30) cc_final: 0.8349 (m-30) REVERT: B 329 GLU cc_start: 0.7595 (tp30) cc_final: 0.7341 (tp30) REVERT: B 337 GLU cc_start: 0.8622 (tt0) cc_final: 0.8302 (tm-30) REVERT: C 135 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.8993 (mmt90) REVERT: C 290 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8893 (p) REVERT: D 219 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8645 (mmtm) REVERT: D 435 LYS cc_start: 0.9049 (tppt) cc_final: 0.8595 (tppt) REVERT: E 125 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: E 390 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8242 (t80) REVERT: F 390 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8617 (t80) REVERT: F 548 MET cc_start: 0.9117 (tmm) cc_final: 0.8840 (tmm) REVERT: A 142 MET cc_start: 0.8635 (mmm) cc_final: 0.8328 (mmm) REVERT: A 165 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: A 337 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8375 (tt0) outliers start: 61 outliers final: 44 residues processed: 182 average time/residue: 0.1347 time to fit residues: 39.9470 Evaluate side-chains 178 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 CYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 496 LYS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 390 PHE Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 532 MET Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 109 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 179 optimal weight: 0.0670 chunk 242 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 161 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 overall best weight: 2.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.057593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.046590 restraints weight = 70747.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.048415 restraints weight = 31966.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.049612 restraints weight = 18514.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.050420 restraints weight = 12444.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.050961 restraints weight = 9238.057| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20946 Z= 0.125 Angle : 0.491 7.843 28428 Z= 0.259 Chirality : 0.043 0.147 3222 Planarity : 0.004 0.053 3690 Dihedral : 4.044 16.241 2850 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.98 % Allowed : 16.53 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.16), residues: 2628 helix: 1.85 (0.22), residues: 552 sheet: 0.27 (0.18), residues: 778 loop : -1.18 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 340 TYR 0.010 0.001 TYR F 238 PHE 0.012 0.001 PHE F 172 TRP 0.005 0.001 TRP F 525 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00286 (20946) covalent geometry : angle 0.49063 (28428) hydrogen bonds : bond 0.04200 ( 745) hydrogen bonds : angle 4.62737 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 129 time to evaluate : 0.814 Fit side-chains REVERT: B 126 MET cc_start: 0.8095 (mmm) cc_final: 0.7772 (mmm) REVERT: B 167 ASP cc_start: 0.8673 (m-30) cc_final: 0.8467 (m-30) REVERT: B 329 GLU cc_start: 0.7599 (tp30) cc_final: 0.7382 (tp30) REVERT: B 337 GLU cc_start: 0.8690 (tt0) cc_final: 0.8356 (tm-30) REVERT: C 135 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8999 (mmt90) REVERT: C 290 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8895 (p) REVERT: D 435 LYS cc_start: 0.9075 (tppt) cc_final: 0.8578 (tppt) REVERT: E 125 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: E 390 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8277 (t80) REVERT: F 390 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8646 (t80) REVERT: F 407 ASP cc_start: 0.9126 (m-30) cc_final: 0.8651 (m-30) REVERT: F 532 MET cc_start: 0.8499 (ttm) cc_final: 0.8261 (mtt) REVERT: F 548 MET cc_start: 0.9155 (tmm) cc_final: 0.8839 (tmm) REVERT: A 142 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8302 (mmm) REVERT: A 165 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: A 337 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8476 (tt0) outliers start: 66 outliers final: 46 residues processed: 181 average time/residue: 0.1307 time to fit residues: 38.3626 Evaluate side-chains 181 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 CYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 496 LYS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 390 PHE Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 75 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 243 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 103 optimal weight: 0.0270 overall best weight: 3.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.056496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.045492 restraints weight = 71788.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.047291 restraints weight = 32276.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.048473 restraints weight = 18761.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.049262 restraints weight = 12643.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.049803 restraints weight = 9441.011| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20946 Z= 0.163 Angle : 0.519 9.213 28428 Z= 0.275 Chirality : 0.044 0.153 3222 Planarity : 0.004 0.054 3690 Dihedral : 4.214 16.632 2850 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.89 % Allowed : 16.80 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.16), residues: 2628 helix: 1.70 (0.22), residues: 558 sheet: 0.17 (0.18), residues: 779 loop : -1.20 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 340 TYR 0.013 0.001 TYR C 357 PHE 0.012 0.001 PHE F 172 TRP 0.004 0.001 TRP F 525 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00378 (20946) covalent geometry : angle 0.51866 (28428) hydrogen bonds : bond 0.04703 ( 745) hydrogen bonds : angle 4.72651 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 130 time to evaluate : 0.950 Fit side-chains REVERT: B 329 GLU cc_start: 0.7636 (tp30) cc_final: 0.7410 (tp30) REVERT: B 337 GLU cc_start: 0.8696 (tt0) cc_final: 0.8370 (tm-30) REVERT: C 135 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.9028 (mmt90) REVERT: C 290 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8878 (p) REVERT: D 135 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8599 (ptp-170) REVERT: D 435 LYS cc_start: 0.9047 (tppt) cc_final: 0.8536 (tppt) REVERT: E 125 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: E 390 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8416 (t80) REVERT: F 390 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8435 (t80) REVERT: F 407 ASP cc_start: 0.9195 (m-30) cc_final: 0.8719 (m-30) REVERT: F 532 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8427 (mtt) REVERT: F 548 MET cc_start: 0.9227 (tmm) cc_final: 0.8990 (tmm) REVERT: A 142 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8252 (mmm) REVERT: A 165 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7600 (mp10) outliers start: 64 outliers final: 48 residues processed: 179 average time/residue: 0.1320 time to fit residues: 38.2948 Evaluate side-chains 184 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 CYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 496 LYS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 390 PHE Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 532 MET Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 260 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.054576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.043618 restraints weight = 72164.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.045331 restraints weight = 32907.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.046494 restraints weight = 19434.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.047290 restraints weight = 13108.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.047813 restraints weight = 9722.402| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 20946 Z= 0.219 Angle : 0.568 10.900 28428 Z= 0.301 Chirality : 0.045 0.162 3222 Planarity : 0.004 0.054 3690 Dihedral : 4.530 17.057 2850 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.89 % Allowed : 17.16 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.16), residues: 2628 helix: 1.43 (0.22), residues: 576 sheet: 0.15 (0.18), residues: 772 loop : -1.31 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 411 TYR 0.013 0.002 TYR D 357 PHE 0.012 0.001 PHE F 172 TRP 0.005 0.001 TRP B 393 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00510 (20946) covalent geometry : angle 0.56785 (28428) hydrogen bonds : bond 0.05378 ( 745) hydrogen bonds : angle 4.93454 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 0.862 Fit side-chains REVERT: B 167 ASP cc_start: 0.8806 (m-30) cc_final: 0.8449 (m-30) REVERT: B 329 GLU cc_start: 0.7624 (tp30) cc_final: 0.7362 (tp30) REVERT: B 337 GLU cc_start: 0.8723 (tt0) cc_final: 0.8368 (tm-30) REVERT: C 135 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8958 (mmt90) REVERT: C 290 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8826 (p) REVERT: D 135 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8585 (ptp-170) REVERT: D 435 LYS cc_start: 0.9070 (tppt) cc_final: 0.8574 (tppt) REVERT: E 125 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: E 364 MET cc_start: 0.9469 (tpp) cc_final: 0.9225 (tpp) REVERT: E 390 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8395 (t80) REVERT: F 390 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8411 (t80) REVERT: F 532 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8455 (mtt) REVERT: F 536 ASN cc_start: 0.8888 (m110) cc_final: 0.8603 (p0) REVERT: A 133 VAL cc_start: 0.9199 (m) cc_final: 0.8893 (p) REVERT: A 142 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: A 165 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: A 316 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8610 (ttmt) outliers start: 64 outliers final: 48 residues processed: 179 average time/residue: 0.1360 time to fit residues: 39.5785 Evaluate side-chains 182 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 CYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 496 LYS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 390 PHE Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 532 MET Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 100 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.055528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.044617 restraints weight = 71752.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.046389 restraints weight = 32507.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.047550 restraints weight = 18854.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.048343 restraints weight = 12705.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.048890 restraints weight = 9408.825| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20946 Z= 0.154 Angle : 0.522 8.675 28428 Z= 0.277 Chirality : 0.044 0.152 3222 Planarity : 0.004 0.054 3690 Dihedral : 4.319 18.127 2850 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.57 % Allowed : 17.57 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.16), residues: 2628 helix: 1.47 (0.22), residues: 576 sheet: 0.06 (0.18), residues: 785 loop : -1.26 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 411 TYR 0.013 0.001 TYR F 238 PHE 0.011 0.001 PHE F 172 TRP 0.005 0.001 TRP F 525 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00357 (20946) covalent geometry : angle 0.52232 (28428) hydrogen bonds : bond 0.04707 ( 745) hydrogen bonds : angle 4.78112 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.958 Fit side-chains REVERT: B 337 GLU cc_start: 0.8696 (tt0) cc_final: 0.8365 (tm-30) REVERT: C 135 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8874 (mmt90) REVERT: C 493 ASN cc_start: 0.8719 (m110) cc_final: 0.8480 (m-40) REVERT: D 135 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8546 (ptp-170) REVERT: D 435 LYS cc_start: 0.9046 (tppt) cc_final: 0.8538 (tppt) REVERT: E 125 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: E 390 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8296 (t80) REVERT: F 390 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8370 (t80) REVERT: F 548 MET cc_start: 0.9143 (tmm) cc_final: 0.8806 (tmm) REVERT: A 133 VAL cc_start: 0.9132 (m) cc_final: 0.8811 (p) REVERT: A 165 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7522 (mp10) outliers start: 57 outliers final: 45 residues processed: 172 average time/residue: 0.1426 time to fit residues: 39.8111 Evaluate side-chains 173 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 269 CYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 496 LYS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 390 PHE Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 68 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.053465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.042540 restraints weight = 73336.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.044258 restraints weight = 33468.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.045405 restraints weight = 19547.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.046178 restraints weight = 13220.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.046688 restraints weight = 9865.673| |-----------------------------------------------------------------------------| r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 20946 Z= 0.303 Angle : 0.638 12.609 28428 Z= 0.339 Chirality : 0.046 0.171 3222 Planarity : 0.005 0.054 3690 Dihedral : 4.802 18.352 2850 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.48 % Allowed : 17.57 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2628 helix: 1.30 (0.22), residues: 575 sheet: 0.06 (0.18), residues: 760 loop : -1.46 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 411 TYR 0.022 0.002 TYR C 405 PHE 0.015 0.001 PHE D 218 TRP 0.009 0.002 TRP F 393 HIS 0.007 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00707 (20946) covalent geometry : angle 0.63761 (28428) hydrogen bonds : bond 0.05948 ( 745) hydrogen bonds : angle 5.14539 ( 2142) =============================================================================== Job complete usr+sys time: 2651.18 seconds wall clock time: 47 minutes 4.73 seconds (2824.73 seconds total)