Starting phenix.real_space_refine on Sat Sep 12 11:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e7y_9001/09_2026/6e7y_9001.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e7y_9001/09_2026/6e7y_9001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e7y_9001/09_2026/6e7y_9001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e7y_9001/09_2026/6e7y_9001.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e7y_9001/09_2026/6e7y_9001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e7y_9001/09_2026/6e7y_9001.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.044 sd= 0.457 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 100 5.16 5 C 10104 2.51 5 N 2560 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15508 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.95, per 1000 atoms: 0.25 Number of scatterers: 15508 At special positions: 0 Unit cell: (126.26, 125.19, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 12 15.00 O 2732 8.00 N 2560 7.00 C 10104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.04 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: 1.27 Conformation dependent library (CDL) restraints added in 656.1 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 53.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 removed outlier: 3.723A pdb=" N LYS A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.834A pdb=" N ALA A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 66 through 93 removed outlier: 3.896A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 106 removed outlier: 3.616A pdb=" N THR A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.670A pdb=" N VAL A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.533A pdb=" N PHE A 297 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 298 " --> pdb=" O ASN A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 298' Processing helix chain 'A' and resid 301 through 334 removed outlier: 4.025A pdb=" N VAL A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 374 removed outlier: 3.637A pdb=" N THR A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.917A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.936A pdb=" N TYR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 removed outlier: 3.647A pdb=" N THR A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.582A pdb=" N CYS A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.587A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS A 440 " --> pdb=" O TYR A 436 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.557A pdb=" N SER A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.731A pdb=" N GLN A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 487 through 501 removed outlier: 4.039A pdb=" N TRP A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 520 removed outlier: 3.790A pdb=" N PHE A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.713A pdb=" N ILE A 524 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 525 " --> pdb=" O ASP A 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 525' Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.723A pdb=" N LYS B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.833A pdb=" N ALA B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'B' and resid 66 through 93 removed outlier: 3.896A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 106 removed outlier: 3.617A pdb=" N THR B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.669A pdb=" N VAL B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 removed outlier: 3.534A pdb=" N PHE B 297 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 298 " --> pdb=" O ASN B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 298' Processing helix chain 'B' and resid 301 through 334 removed outlier: 4.024A pdb=" N VAL B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 374 removed outlier: 3.637A pdb=" N THR B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.917A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 3.936A pdb=" N TYR B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 removed outlier: 3.648A pdb=" N THR B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.582A pdb=" N CYS B 430 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.587A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 440 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.559A pdb=" N SER B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 481 removed outlier: 3.731A pdb=" N GLN B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 487 through 501 removed outlier: 4.040A pdb=" N TRP B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 520 removed outlier: 3.790A pdb=" N PHE B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.714A pdb=" N ILE B 524 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 525 " --> pdb=" O ASP B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 521 through 525' Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.723A pdb=" N LYS C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 54 through 59 removed outlier: 3.834A pdb=" N ALA C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 54 through 59' Processing helix chain 'C' and resid 66 through 93 removed outlier: 3.896A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 removed outlier: 3.616A pdb=" N THR C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.670A pdb=" N VAL C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 298 removed outlier: 3.534A pdb=" N PHE C 297 " --> pdb=" O ASP C 294 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 298 " --> pdb=" O ASN C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 294 through 298' Processing helix chain 'C' and resid 301 through 334 removed outlier: 4.025A pdb=" N VAL C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN C 328 " --> pdb=" O PHE C 324 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 374 removed outlier: 3.636A pdb=" N THR C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 399 removed outlier: 3.918A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 removed outlier: 3.936A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 431 removed outlier: 3.648A pdb=" N THR C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.582A pdb=" N CYS C 430 " --> pdb=" O MET C 426 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.587A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS C 440 " --> pdb=" O TYR C 436 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 446 " --> pdb=" O CYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 464 removed outlier: 3.558A pdb=" N SER C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 481 removed outlier: 3.730A pdb=" N GLN C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'C' and resid 487 through 501 removed outlier: 4.040A pdb=" N TRP C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 removed outlier: 3.790A pdb=" N PHE C 513 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.713A pdb=" N ILE C 524 " --> pdb=" O TYR C 521 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 525 " --> pdb=" O ASP C 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 521 through 525' Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.723A pdb=" N LYS D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 54 through 59 removed outlier: 3.834A pdb=" N ALA D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'D' and resid 66 through 93 removed outlier: 3.896A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.615A pdb=" N THR D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 135 Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.670A pdb=" N VAL D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.534A pdb=" N PHE D 297 " --> pdb=" O ASP D 294 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 298 " --> pdb=" O ASN D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 294 through 298' Processing helix chain 'D' and resid 301 through 334 removed outlier: 4.024A pdb=" N VAL D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 374 removed outlier: 3.636A pdb=" N THR D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 399 removed outlier: 3.918A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 407 removed outlier: 3.937A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 431 removed outlier: 3.648A pdb=" N THR D 417 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.583A pdb=" N CYS D 430 " --> pdb=" O MET D 426 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.587A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS D 440 " --> pdb=" O TYR D 436 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 446 " --> pdb=" O CYS D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 464 removed outlier: 3.558A pdb=" N SER D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 481 removed outlier: 3.730A pdb=" N GLN D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'D' and resid 487 through 501 removed outlier: 4.040A pdb=" N TRP D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 520 removed outlier: 3.790A pdb=" N PHE D 513 " --> pdb=" O VAL D 509 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 525 removed outlier: 3.713A pdb=" N ILE D 524 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 525 " --> pdb=" O ASP D 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 521 through 525' Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.602A pdb=" N ILE A 271 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 263 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 274 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 235 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG A 168 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 240 removed outlier: 3.962A pdb=" N CYS A 253 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN A 282 " --> pdb=" O CYS A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.602A pdb=" N ILE B 271 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 263 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 274 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 235 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG B 168 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 238 through 240 removed outlier: 3.961A pdb=" N CYS B 253 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN B 282 " --> pdb=" O CYS B 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.601A pdb=" N ILE C 271 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 263 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 274 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 235 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG C 168 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 240 removed outlier: 3.962A pdb=" N CYS C 253 " --> pdb=" O GLN C 282 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN C 282 " --> pdb=" O CYS C 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.602A pdb=" N ILE D 271 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 263 " --> pdb=" O PRO D 272 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 274 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 235 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG D 168 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 238 through 240 removed outlier: 3.962A pdb=" N CYS D 253 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN D 282 " --> pdb=" O CYS D 253 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1512 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: 2.66 Time building geometry restraints manager: 1.71 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: 4718 1.34 - 1.46: 3751 1.46 - 1.58: 7243 1.58 - 1.70: 36 1.70 - 1.82: 140 Bond restraints: 15888 Sorted by residual: bond pdb=" C1A PIO A 801 " pdb=" O2C PIO A 801 " ideal model delta sigma weight residual 1.332 1.456 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C1A PIO B 801 " pdb=" O2C PIO B 801 " ideal model delta sigma weight residual 1.332 1.455 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C1A PIO C 801 " pdb=" O2C PIO C 801 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C1A PIO D 801 " pdb=" O2C PIO D 801 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C1B PIO D 801 " pdb=" O3C PIO D 801 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 15883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 21072 2.48 - 4.96: 366 4.96 - 7.44: 78 7.44 - 9.91: 40 9.91 - 12.39: 8 Bond angle restraints: 21564 Sorted by residual: angle pdb=" C PRO A 177 " pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" C PRO B 177 " pdb=" N ALA B 178 " pdb=" CA ALA B 178 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C PRO C 177 " pdb=" N ALA C 178 " pdb=" CA ALA C 178 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C PRO D 177 " pdb=" N ALA D 178 " pdb=" CA ALA D 178 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" O1 PIO A 801 " pdb=" P1 PIO A 801 " pdb=" O13 PIO A 801 " ideal model delta sigma weight residual 97.64 110.03 -12.39 3.00e+00 1.11e-01 1.71e+01 ... (remaining 21559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 8644 14.17 - 28.34: 448 28.34 - 42.51: 136 42.51 - 56.68: 24 56.68 - 70.85: 16 Dihedral angle restraints: 9268 sinusoidal: 3704 harmonic: 5564 Sorted by residual: dihedral pdb=" CB CYS C 253 " pdb=" SG CYS C 253 " pdb=" SG CYS C 284 " pdb=" CB CYS C 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.59 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS B 253 " pdb=" SG CYS B 253 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.61 53.39 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS A 253 " pdb=" SG CYS A 253 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.65 53.35 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 9265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1263 0.032 - 0.065: 799 0.065 - 0.097: 291 0.097 - 0.129: 83 0.129 - 0.162: 24 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CB VAL C 289 " pdb=" CA VAL C 289 " pdb=" CG1 VAL C 289 " pdb=" CG2 VAL C 289 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA LEU C 139 " pdb=" N LEU C 139 " pdb=" C LEU C 139 " pdb=" CB LEU C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA LEU D 139 " pdb=" N LEU D 139 " pdb=" C LEU D 139 " pdb=" CB LEU D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2457 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 422 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO D 423 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 422 " -0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 423 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 422 " -0.037 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO C 423 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 423 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 423 " -0.031 5.00e-02 4.00e+02 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5266 2.87 - 3.38: 13651 3.38 - 3.89: 22911 3.89 - 4.39: 25957 4.39 - 4.90: 44955 Nonbonded interactions: 112740 Sorted by model distance: nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.364 3.040 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.364 3.040 nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.365 3.040 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.365 3.040 nonbonded pdb=" NE2 GLN D 69 " pdb=" OG SER D 312 " model vdw 2.376 3.120 ... (remaining 112735 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.006 0.124 15896 Z= 0.299 Angle : 0.922 12.393 21580 Z= 0.448 Chirality : 0.047 0.162 2460 Planarity : 0.006 0.055 2656 Dihedral : 10.092 70.849 5660 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -5.91 (0.13), residues: 1884 helix: -4.54 (0.06), residues: 924 sheet: -1.60 (0.37), residues: 168 loop : -3.49 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 427 TYR 0.013 0.001 TYR B 218 PHE 0.019 0.002 PHE A 477 TRP 0.015 0.001 TRP C 157 HIS 0.006 0.001 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.30 (15888) covalent geometry : angle 0.92117 / 0.45 (21564) SS BOND : bond 0.00432 / 0.21 ( 8) SS BOND : angle 1.35245 / 0.71 ( 16) hydrogen bonds : bond 0.34035 / 21.43 ( 520) hydrogen bonds : angle 11.15272 / 7.67 ( 1512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.605 Fit side-chains REVERT: A 57 ARG cc_start: 0.7242 (ttm170) cc_final: 0.7008 (mtt-85) REVERT: A 510 LEU cc_start: 0.8652 (tp) cc_final: 0.8338 (tt) REVERT: B 57 ARG cc_start: 0.7326 (ttm170) cc_final: 0.7076 (mtt-85) REVERT: B 510 LEU cc_start: 0.8639 (tp) cc_final: 0.8351 (tt) REVERT: C 510 LEU cc_start: 0.8720 (tp) cc_final: 0.8386 (tt) REVERT: D 349 GLU cc_start: 0.8685 (tp30) cc_final: 0.8361 (mm-30) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.1330 time to fit residues: 98.5557 Evaluate side-chains 240 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN A 103 HIS A 234 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 292 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN B 97 ASN B 103 HIS B 234 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 292 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN C 97 ASN C 103 HIS C 234 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS C 292 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN D 97 ASN D 103 HIS D 234 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS D 292 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115239 restraints weight = 26207.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117791 restraints weight = 15469.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119428 restraints weight = 11388.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120398 restraints weight = 9561.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120687 restraints weight = 8654.018| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15896 Z= 0.125 Angle : 0.620 8.414 21580 Z= 0.311 Chirality : 0.042 0.186 2460 Planarity : 0.005 0.040 2656 Dihedral : 7.408 58.980 2156 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.37 % Allowed : 11.58 % Favored : 85.05 % 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: -4.13 (0.16), residues: 1884 helix: -2.78 (0.12), residues: 936 sheet: -1.09 (0.38), residues: 204 loop : -2.99 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 172 TYR 0.013 0.001 TYR A 436 PHE 0.010 0.001 PHE C 493 TRP 0.007 0.001 TRP A 157 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15888) covalent geometry : angle 0.61880 / 0.31 (21564) SS BOND : bond 0.00865 / 0.38 ( 8) SS BOND : angle 1.71356 / 0.90 ( 16) hydrogen bonds : bond 0.04672 / 2.96 ( 520) hydrogen bonds : angle 4.99986 / 3.47 ( 1512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 249 time to evaluate : 0.624 Fit side-chains REVERT: A 57 ARG cc_start: 0.7421 (ttm170) cc_final: 0.7085 (mtt90) REVERT: A 134 ASP cc_start: 0.7485 (m-30) cc_final: 0.7245 (m-30) REVERT: B 57 ARG cc_start: 0.7431 (ttm170) cc_final: 0.7124 (mtt90) REVERT: B 134 ASP cc_start: 0.7503 (m-30) cc_final: 0.7299 (m-30) REVERT: B 350 PHE cc_start: 0.7292 (m-10) cc_final: 0.7076 (m-10) REVERT: D 89 LEU cc_start: 0.8609 (tp) cc_final: 0.8279 (tt) REVERT: D 134 ASP cc_start: 0.7486 (m-30) cc_final: 0.7269 (m-30) REVERT: D 350 PHE cc_start: 0.7268 (m-10) cc_final: 0.7007 (m-10) outliers start: 57 outliers final: 36 residues processed: 288 average time/residue: 0.1072 time to fit residues: 49.2843 Evaluate side-chains 256 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 185 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 267 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN B 135 GLN B 267 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN C 135 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN D 135 GLN D 267 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106505 restraints weight = 26518.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108878 restraints weight = 16050.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110318 restraints weight = 12060.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111313 restraints weight = 10273.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111562 restraints weight = 9295.194| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15896 Z= 0.234 Angle : 0.674 12.916 21580 Z= 0.339 Chirality : 0.045 0.195 2460 Planarity : 0.005 0.038 2656 Dihedral : 7.176 54.685 2156 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.14 % Allowed : 12.47 % Favored : 83.39 % 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: -3.15 (0.18), residues: 1884 helix: -1.53 (0.15), residues: 956 sheet: -1.49 (0.36), residues: 216 loop : -2.94 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 102 TYR 0.015 0.002 TYR C 497 PHE 0.021 0.002 PHE A 83 TRP 0.010 0.002 TRP D 157 HIS 0.014 0.002 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (15888) covalent geometry : angle 0.67300 / 0.34 (21564) SS BOND : bond 0.00948 / 0.52 ( 8) SS BOND : angle 1.70060 / 0.92 ( 16) hydrogen bonds : bond 0.04913 / 3.12 ( 520) hydrogen bonds : angle 4.53753 / 3.19 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 214 time to evaluate : 0.652 Fit side-chains REVERT: A 57 ARG cc_start: 0.7621 (ttm170) cc_final: 0.7141 (mtt-85) REVERT: A 89 LEU cc_start: 0.8673 (tp) cc_final: 0.8462 (tt) REVERT: A 115 ASP cc_start: 0.7827 (p0) cc_final: 0.7541 (p0) REVERT: B 57 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7108 (mtt-85) REVERT: B 89 LEU cc_start: 0.8685 (tp) cc_final: 0.8454 (tt) REVERT: B 115 ASP cc_start: 0.7880 (p0) cc_final: 0.7589 (p0) REVERT: B 134 ASP cc_start: 0.7641 (m-30) cc_final: 0.7378 (m-30) REVERT: B 350 PHE cc_start: 0.7360 (m-10) cc_final: 0.7153 (m-10) REVERT: C 89 LEU cc_start: 0.8685 (tp) cc_final: 0.8462 (tt) REVERT: C 115 ASP cc_start: 0.7831 (p0) cc_final: 0.7550 (p0) REVERT: D 59 LYS cc_start: 0.4914 (ttmp) cc_final: 0.4706 (mttt) REVERT: D 89 LEU cc_start: 0.8624 (tp) cc_final: 0.8387 (tt) REVERT: D 115 ASP cc_start: 0.7859 (p0) cc_final: 0.7583 (p0) REVERT: D 134 ASP cc_start: 0.7679 (m-30) cc_final: 0.7412 (m-30) REVERT: D 350 PHE cc_start: 0.7391 (m-10) cc_final: 0.7148 (m-10) outliers start: 70 outliers final: 52 residues processed: 257 average time/residue: 0.1184 time to fit residues: 47.2894 Evaluate side-chains 244 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN D 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108573 restraints weight = 26307.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111035 restraints weight = 15975.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112622 restraints weight = 11914.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113366 restraints weight = 10045.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113834 restraints weight = 9188.527| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15896 Z= 0.125 Angle : 0.589 11.112 21580 Z= 0.285 Chirality : 0.042 0.175 2460 Planarity : 0.004 0.037 2656 Dihedral : 6.627 51.212 2156 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.55 % Allowed : 13.06 % Favored : 83.39 % 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: -2.45 (0.18), residues: 1884 helix: -0.90 (0.16), residues: 960 sheet: -0.86 (0.38), residues: 200 loop : -2.79 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.011 0.001 TYR A 497 PHE 0.008 0.001 PHE A 83 TRP 0.007 0.001 TRP A 398 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (15888) covalent geometry : angle 0.58827 / 0.28 (21564) SS BOND : bond 0.00621 / 0.35 ( 8) SS BOND : angle 1.49471 / 0.78 ( 16) hydrogen bonds : bond 0.03599 / 2.29 ( 520) hydrogen bonds : angle 4.14084 / 2.90 ( 1512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 0.612 Fit side-chains REVERT: A 57 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7160 (mtt-85) REVERT: A 89 LEU cc_start: 0.8663 (tp) cc_final: 0.8456 (tt) REVERT: B 57 ARG cc_start: 0.7625 (ttm170) cc_final: 0.7126 (mtt-85) REVERT: B 89 LEU cc_start: 0.8684 (tp) cc_final: 0.8453 (tt) REVERT: B 350 PHE cc_start: 0.7391 (m-10) cc_final: 0.7171 (m-10) REVERT: C 89 LEU cc_start: 0.8620 (tp) cc_final: 0.8408 (tt) REVERT: C 115 ASP cc_start: 0.7742 (p0) cc_final: 0.7507 (p0) REVERT: D 89 LEU cc_start: 0.8643 (tp) cc_final: 0.8413 (tt) REVERT: D 115 ASP cc_start: 0.7769 (p0) cc_final: 0.7536 (p0) REVERT: D 350 PHE cc_start: 0.7399 (m-10) cc_final: 0.7165 (m-10) outliers start: 60 outliers final: 45 residues processed: 246 average time/residue: 0.1112 time to fit residues: 43.6289 Evaluate side-chains 237 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 106 optimal weight: 0.7980 chunk 49 optimal weight: 0.0000 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN B 327 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109009 restraints weight = 26310.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111461 restraints weight = 16163.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113011 restraints weight = 12154.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113729 restraints weight = 10307.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114478 restraints weight = 9457.605| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15896 Z= 0.115 Angle : 0.606 12.652 21580 Z= 0.290 Chirality : 0.042 0.171 2460 Planarity : 0.004 0.035 2656 Dihedral : 6.332 52.188 2156 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.37 % Allowed : 13.48 % Favored : 83.16 % 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: -1.78 (0.19), residues: 1884 helix: -0.45 (0.17), residues: 964 sheet: 0.00 (0.42), residues: 180 loop : -2.45 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 172 TYR 0.011 0.001 TYR B 497 PHE 0.008 0.001 PHE B 474 TRP 0.007 0.001 TRP A 398 HIS 0.005 0.001 HIS D 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.11 (15888) covalent geometry : angle 0.60062 / 0.29 (21564) SS BOND : bond 0.01085 / 0.62 ( 8) SS BOND : angle 3.13721 / 1.65 ( 16) hydrogen bonds : bond 0.03294 / 2.11 ( 520) hydrogen bonds : angle 3.99456 / 2.80 ( 1512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 0.608 Fit side-chains REVERT: A 57 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7117 (mtt-85) REVERT: A 89 LEU cc_start: 0.8633 (tp) cc_final: 0.8421 (tt) REVERT: A 134 ASP cc_start: 0.7582 (m-30) cc_final: 0.7348 (m-30) REVERT: B 57 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7130 (mtt-85) REVERT: B 89 LEU cc_start: 0.8650 (tp) cc_final: 0.8403 (tt) REVERT: B 134 ASP cc_start: 0.7562 (m-30) cc_final: 0.7341 (m-30) REVERT: C 89 LEU cc_start: 0.8636 (tp) cc_final: 0.8422 (tt) REVERT: D 89 LEU cc_start: 0.8646 (tp) cc_final: 0.8410 (tt) REVERT: D 115 ASP cc_start: 0.7748 (p0) cc_final: 0.7544 (p0) REVERT: D 240 ILE cc_start: 0.9104 (mm) cc_final: 0.8861 (tt) outliers start: 57 outliers final: 42 residues processed: 245 average time/residue: 0.1108 time to fit residues: 43.0767 Evaluate side-chains 237 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107215 restraints weight = 26039.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109622 restraints weight = 16049.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111168 restraints weight = 12131.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111984 restraints weight = 10307.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112153 restraints weight = 9430.926| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15896 Z= 0.151 Angle : 0.632 13.880 21580 Z= 0.307 Chirality : 0.043 0.200 2460 Planarity : 0.004 0.037 2656 Dihedral : 6.186 50.737 2156 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.90 % Allowed : 12.65 % Favored : 83.45 % 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: -1.54 (0.20), residues: 1884 helix: -0.23 (0.17), residues: 964 sheet: 0.43 (0.46), residues: 160 loop : -2.40 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 172 TYR 0.014 0.001 TYR A 497 PHE 0.010 0.001 PHE B 83 TRP 0.007 0.001 TRP B 398 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (15888) covalent geometry : angle 0.62732 / 0.30 (21564) SS BOND : bond 0.01065 / 0.60 ( 8) SS BOND : angle 2.99236 / 1.56 ( 16) hydrogen bonds : bond 0.03573 / 2.30 ( 520) hydrogen bonds : angle 3.97173 / 2.79 ( 1512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 193 time to evaluate : 0.652 Fit side-chains REVERT: A 57 ARG cc_start: 0.7645 (ttm170) cc_final: 0.7115 (mtt-85) REVERT: A 115 ASP cc_start: 0.7787 (p0) cc_final: 0.7433 (p0) REVERT: A 134 ASP cc_start: 0.7591 (m-30) cc_final: 0.7349 (m-30) REVERT: B 57 ARG cc_start: 0.7678 (ttm170) cc_final: 0.7093 (mtt-85) REVERT: B 89 LEU cc_start: 0.8674 (tp) cc_final: 0.8471 (tt) REVERT: B 115 ASP cc_start: 0.7934 (p0) cc_final: 0.7653 (p0) REVERT: B 134 ASP cc_start: 0.7621 (m-30) cc_final: 0.7392 (m-30) REVERT: B 348 LEU cc_start: 0.7832 (pp) cc_final: 0.7583 (pp) REVERT: C 240 ILE cc_start: 0.9112 (mm) cc_final: 0.8870 (tt) REVERT: C 405 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8503 (mp) REVERT: D 240 ILE cc_start: 0.9117 (mm) cc_final: 0.8893 (tt) outliers start: 66 outliers final: 59 residues processed: 238 average time/residue: 0.1132 time to fit residues: 42.7467 Evaluate side-chains 248 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 188 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109493 restraints weight = 25998.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111936 restraints weight = 15866.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113534 restraints weight = 11914.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114492 restraints weight = 10098.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114500 restraints weight = 9187.796| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15896 Z= 0.102 Angle : 0.591 12.559 21580 Z= 0.282 Chirality : 0.042 0.182 2460 Planarity : 0.003 0.036 2656 Dihedral : 5.971 53.758 2156 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.07 % Allowed : 13.89 % Favored : 83.04 % 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: -1.30 (0.20), residues: 1884 helix: -0.04 (0.17), residues: 980 sheet: 0.60 (0.47), residues: 160 loop : -2.33 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 172 TYR 0.010 0.001 TYR A 497 PHE 0.008 0.001 PHE C 474 TRP 0.007 0.001 TRP A 398 HIS 0.003 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (15888) covalent geometry : angle 0.58739 / 0.28 (21564) SS BOND : bond 0.01011 / 0.58 ( 8) SS BOND : angle 2.52747 / 1.29 ( 16) hydrogen bonds : bond 0.03027 / 1.95 ( 520) hydrogen bonds : angle 3.81710 / 2.68 ( 1512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.622 Fit side-chains REVERT: A 57 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7102 (mtt-85) REVERT: A 115 ASP cc_start: 0.7746 (p0) cc_final: 0.7456 (p0) REVERT: A 134 ASP cc_start: 0.7575 (m-30) cc_final: 0.7346 (m-30) REVERT: A 320 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8400 (mm) REVERT: B 57 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7126 (mtt-85) REVERT: B 89 LEU cc_start: 0.8685 (tp) cc_final: 0.8480 (tt) REVERT: B 134 ASP cc_start: 0.7556 (m-30) cc_final: 0.7337 (m-30) REVERT: B 348 LEU cc_start: 0.7921 (pp) cc_final: 0.7685 (pp) REVERT: C 115 ASP cc_start: 0.7713 (p0) cc_final: 0.7402 (p0) REVERT: C 134 ASP cc_start: 0.7575 (m-30) cc_final: 0.7349 (m-30) REVERT: C 240 ILE cc_start: 0.9097 (mm) cc_final: 0.8894 (tt) REVERT: C 405 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8465 (mp) REVERT: D 134 ASP cc_start: 0.7557 (m-30) cc_final: 0.7341 (m-30) REVERT: D 327 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6604 (tp40) outliers start: 52 outliers final: 39 residues processed: 231 average time/residue: 0.1128 time to fit residues: 41.1831 Evaluate side-chains 227 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 165 optimal weight: 0.0000 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 131 optimal weight: 0.4980 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 167 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109255 restraints weight = 26215.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111525 restraints weight = 16502.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112987 restraints weight = 12638.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113719 restraints weight = 10836.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113943 restraints weight = 9951.469| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15896 Z= 0.126 Angle : 0.701 16.850 21580 Z= 0.337 Chirality : 0.044 0.283 2460 Planarity : 0.003 0.036 2656 Dihedral : 6.211 52.566 2156 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.61 % Allowed : 13.24 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1884 helix: 0.14 (0.17), residues: 980 sheet: 0.33 (0.47), residues: 160 loop : -2.24 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 57 TYR 0.012 0.001 TYR A 497 PHE 0.008 0.001 PHE C 182 TRP 0.007 0.001 TRP A 398 HIS 0.004 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15888) covalent geometry : angle 0.66667 / 0.32 (21564) SS BOND : bond 0.00336 / 0.17 ( 8) SS BOND : angle 7.94318 / 4.00 ( 16) hydrogen bonds : bond 0.03430 / 2.25 ( 520) hydrogen bonds : angle 3.76265 / 2.66 ( 1512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.622 Fit side-chains REVERT: A 57 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7108 (mtt-85) REVERT: A 115 ASP cc_start: 0.7732 (p0) cc_final: 0.7353 (p0) REVERT: A 134 ASP cc_start: 0.7588 (m-30) cc_final: 0.7355 (m-30) REVERT: A 320 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8402 (mm) REVERT: B 57 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7134 (mtt-85) REVERT: B 89 LEU cc_start: 0.8711 (tp) cc_final: 0.8501 (tt) REVERT: B 134 ASP cc_start: 0.7592 (m-30) cc_final: 0.7378 (m-30) REVERT: B 348 LEU cc_start: 0.7783 (pp) cc_final: 0.7569 (pp) REVERT: C 67 MET cc_start: 0.7838 (mmm) cc_final: 0.7564 (mmm) REVERT: C 115 ASP cc_start: 0.7694 (p0) cc_final: 0.7334 (p0) REVERT: C 134 ASP cc_start: 0.7566 (m-30) cc_final: 0.7339 (m-30) REVERT: C 240 ILE cc_start: 0.9106 (mm) cc_final: 0.8898 (tt) REVERT: C 405 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8461 (mp) REVERT: D 115 ASP cc_start: 0.7801 (p0) cc_final: 0.7503 (p0) REVERT: D 134 ASP cc_start: 0.7569 (m-30) cc_final: 0.7361 (m-30) outliers start: 61 outliers final: 45 residues processed: 241 average time/residue: 0.1093 time to fit residues: 41.8044 Evaluate side-chains 236 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 161 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.0770 chunk 114 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110289 restraints weight = 26190.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112588 restraints weight = 16501.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114093 restraints weight = 12649.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114900 restraints weight = 10821.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115261 restraints weight = 9927.378| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15896 Z= 0.105 Angle : 0.649 12.879 21580 Z= 0.310 Chirality : 0.043 0.229 2460 Planarity : 0.003 0.035 2656 Dihedral : 6.037 54.569 2156 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.66 % Allowed : 14.13 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.90 (0.20), residues: 1884 helix: 0.39 (0.18), residues: 952 sheet: 0.27 (0.47), residues: 160 loop : -2.07 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 57 TYR 0.010 0.001 TYR B 497 PHE 0.008 0.001 PHE C 182 TRP 0.007 0.001 TRP B 398 HIS 0.003 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (15888) covalent geometry : angle 0.62109 / 0.30 (21564) SS BOND : bond 0.00496 / 0.25 ( 8) SS BOND : angle 6.98039 / 3.51 ( 16) hydrogen bonds : bond 0.02991 / 1.94 ( 520) hydrogen bonds : angle 3.68605 / 2.61 ( 1512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.625 Fit side-chains REVERT: A 57 ARG cc_start: 0.7597 (ttm170) cc_final: 0.7104 (mtt-85) REVERT: A 67 MET cc_start: 0.7725 (mmm) cc_final: 0.7491 (mmm) REVERT: A 115 ASP cc_start: 0.7731 (p0) cc_final: 0.7451 (p0) REVERT: A 134 ASP cc_start: 0.7600 (m-30) cc_final: 0.7380 (m-30) REVERT: A 320 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8357 (mm) REVERT: B 57 ARG cc_start: 0.7629 (ttm170) cc_final: 0.7135 (mtt-85) REVERT: B 67 MET cc_start: 0.7756 (mmm) cc_final: 0.7526 (mmm) REVERT: B 89 LEU cc_start: 0.8719 (tp) cc_final: 0.8507 (tt) REVERT: B 115 ASP cc_start: 0.7747 (p0) cc_final: 0.7443 (p0) REVERT: B 134 ASP cc_start: 0.7580 (m-30) cc_final: 0.7372 (m-30) REVERT: B 348 LEU cc_start: 0.7809 (pp) cc_final: 0.7603 (pp) REVERT: C 67 MET cc_start: 0.7823 (mmm) cc_final: 0.7586 (mmm) REVERT: C 115 ASP cc_start: 0.7670 (p0) cc_final: 0.7418 (p0) REVERT: C 134 ASP cc_start: 0.7592 (m-30) cc_final: 0.7376 (m-30) REVERT: C 405 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8451 (mp) REVERT: D 115 ASP cc_start: 0.7731 (p0) cc_final: 0.7416 (p0) REVERT: D 134 ASP cc_start: 0.7587 (m-30) cc_final: 0.7383 (m-30) REVERT: D 327 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6805 (tp40) outliers start: 45 outliers final: 38 residues processed: 241 average time/residue: 0.1067 time to fit residues: 41.1043 Evaluate side-chains 235 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 153 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 ASN D 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109865 restraints weight = 26203.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112345 restraints weight = 16079.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113900 restraints weight = 12113.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114703 restraints weight = 10282.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115305 restraints weight = 9405.133| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15896 Z= 0.100 Angle : 0.619 13.010 21580 Z= 0.296 Chirality : 0.042 0.208 2460 Planarity : 0.003 0.035 2656 Dihedral : 5.895 55.255 2156 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.01 % Allowed : 13.77 % Favored : 83.22 % 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: -0.74 (0.20), residues: 1884 helix: 0.56 (0.18), residues: 952 sheet: 0.38 (0.47), residues: 160 loop : -2.06 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 57 TYR 0.010 0.001 TYR A 497 PHE 0.008 0.001 PHE C 182 TRP 0.007 0.001 TRP D 398 HIS 0.005 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (15888) covalent geometry : angle 0.59313 / 0.28 (21564) SS BOND : bond 0.00215 / 0.10 ( 8) SS BOND : angle 6.53043 / 3.29 ( 16) hydrogen bonds : bond 0.02965 / 1.94 ( 520) hydrogen bonds : angle 3.63470 / 2.57 ( 1512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.935 Fit side-chains REVERT: A 57 ARG cc_start: 0.7656 (ttm170) cc_final: 0.7104 (mtt-85) REVERT: A 67 MET cc_start: 0.7720 (mmm) cc_final: 0.7516 (mmm) REVERT: A 115 ASP cc_start: 0.7741 (p0) cc_final: 0.7488 (p0) REVERT: A 134 ASP cc_start: 0.7596 (m-30) cc_final: 0.7378 (m-30) REVERT: A 240 ILE cc_start: 0.9002 (mm) cc_final: 0.8798 (tt) REVERT: A 320 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8349 (mm) REVERT: B 57 ARG cc_start: 0.7651 (ttm170) cc_final: 0.7146 (mtt-85) REVERT: B 89 LEU cc_start: 0.8727 (tp) cc_final: 0.8511 (tt) REVERT: B 115 ASP cc_start: 0.7780 (p0) cc_final: 0.7497 (p0) REVERT: B 134 ASP cc_start: 0.7573 (m-30) cc_final: 0.7366 (m-30) REVERT: B 348 LEU cc_start: 0.7837 (pp) cc_final: 0.7602 (pp) REVERT: C 67 MET cc_start: 0.7794 (mmm) cc_final: 0.7530 (mmm) REVERT: C 115 ASP cc_start: 0.7705 (p0) cc_final: 0.7443 (p0) REVERT: C 320 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8331 (mm) REVERT: C 351 VAL cc_start: 0.8536 (t) cc_final: 0.8263 (p) REVERT: C 405 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8489 (mp) REVERT: D 115 ASP cc_start: 0.7706 (p0) cc_final: 0.7421 (p0) REVERT: D 320 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8313 (mm) outliers start: 51 outliers final: 41 residues processed: 234 average time/residue: 0.1105 time to fit residues: 41.4334 Evaluate side-chains 238 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105907 restraints weight = 26159.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108291 restraints weight = 16267.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109806 restraints weight = 12320.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110313 restraints weight = 10501.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111146 restraints weight = 9799.768| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15896 Z= 0.189 Angle : 0.691 13.322 21580 Z= 0.335 Chirality : 0.045 0.206 2460 Planarity : 0.004 0.037 2656 Dihedral : 6.124 51.874 2156 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.43 % Allowed : 13.53 % Favored : 83.04 % 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: -0.94 (0.20), residues: 1884 helix: 0.44 (0.18), residues: 948 sheet: -0.11 (0.45), residues: 168 loop : -2.14 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 57 TYR 0.017 0.001 TYR A 497 PHE 0.012 0.001 PHE D 83 TRP 0.009 0.001 TRP B 444 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (15888) covalent geometry : angle 0.66475 / 0.32 (21564) SS BOND : bond 0.00306 / 0.16 ( 8) SS BOND : angle 6.92568 / 3.50 ( 16) hydrogen bonds : bond 0.03680 / 2.37 ( 520) hydrogen bonds : angle 3.87036 / 2.76 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2556.70 seconds wall clock time: 45 minutes 15.80 seconds (2715.80 seconds total)