Starting phenix.real_space_refine on Mon Aug 25 17:32:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8syg_40873/08_2025/8syg_40873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syg_40873/08_2025/8syg_40873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8syg_40873/08_2025/8syg_40873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syg_40873/08_2025/8syg_40873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8syg_40873/08_2025/8syg_40873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syg_40873/08_2025/8syg_40873.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.114 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 S 70 5.16 5 C 9632 2.51 5 N 2730 2.21 5 O 2786 1.98 5 H 14714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29932 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Restraints were copied for chains: A, C, D, E, F, G, H, I, J, K, L, M, N Time building chain proxies: 2.65, per 1000 atoms: 0.09 Number of scatterers: 29932 At special positions: 0 Unit cell: (135.603, 133.38, 71.877, 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 70 16.00 O 2786 8.00 N 2730 7.00 C 9632 6.00 H 14714 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 731.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 14 sheets defined 32.1% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 345 through 364 removed outlier: 4.068A pdb=" N GLU B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 removed outlier: 3.765A pdb=" N ILE C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 381 through 385 Processing helix chain 'C' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR C 398 " --> pdb=" O PHE C 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 364 removed outlier: 3.763A pdb=" N ILE E 350 " --> pdb=" O ARG E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE F 350 " --> pdb=" O ARG F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 372 Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE F 397 " --> pdb=" O ASP F 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 364 removed outlier: 3.765A pdb=" N ILE G 350 " --> pdb=" O ARG G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 372 Processing helix chain 'G' and resid 381 through 385 Processing helix chain 'G' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE H 350 " --> pdb=" O ARG H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 372 Processing helix chain 'H' and resid 381 through 385 Processing helix chain 'H' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE H 397 " --> pdb=" O ASP H 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE I 350 " --> pdb=" O ARG I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 372 Processing helix chain 'I' and resid 381 through 385 Processing helix chain 'I' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE I 397 " --> pdb=" O ASP I 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 364 removed outlier: 3.765A pdb=" N ILE J 350 " --> pdb=" O ARG J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 372 Processing helix chain 'J' and resid 381 through 385 Processing helix chain 'J' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE J 397 " --> pdb=" O ASP J 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR J 398 " --> pdb=" O PHE J 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 372 Processing helix chain 'K' and resid 381 through 385 Processing helix chain 'K' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR K 398 " --> pdb=" O PHE K 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE L 350 " --> pdb=" O ARG L 346 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 372 Processing helix chain 'L' and resid 381 through 385 Processing helix chain 'L' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE L 397 " --> pdb=" O ASP L 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR L 398 " --> pdb=" O PHE L 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE M 350 " --> pdb=" O ARG M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 372 Processing helix chain 'M' and resid 381 through 385 Processing helix chain 'M' and resid 392 through 402 removed outlier: 3.839A pdb=" N PHE M 397 " --> pdb=" O ASP M 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR M 398 " --> pdb=" O PHE M 394 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE N 350 " --> pdb=" O ARG N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 372 Processing helix chain 'N' and resid 381 through 385 Processing helix chain 'N' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE N 397 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR N 398 " --> pdb=" O PHE N 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS B 466 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY B 376 " --> pdb=" O HIS B 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS B 468 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR B 378 " --> pdb=" O HIS B 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER B 470 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE B 380 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 458 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE B 464 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS B 456 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS B 466 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER B 426 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU B 421 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS B 428 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE B 419 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 430 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS A 466 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N GLY A 376 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS A 468 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR A 378 " --> pdb=" O HIS A 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER A 470 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE A 380 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 458 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE A 464 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS A 456 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A 466 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER A 426 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU A 421 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS A 428 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 419 " --> pdb=" O CYS A 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 430 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS C 466 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY C 376 " --> pdb=" O HIS C 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS C 468 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR C 378 " --> pdb=" O HIS C 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER C 470 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N PHE C 380 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG C 458 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE C 464 " --> pdb=" O HIS C 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS C 456 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS C 466 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER C 426 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU C 421 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS C 428 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE C 419 " --> pdb=" O CYS C 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 430 " --> pdb=" O PRO C 417 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS D 466 " --> pdb=" O ASP D 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY D 376 " --> pdb=" O HIS D 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS D 468 " --> pdb=" O GLY D 376 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N THR D 378 " --> pdb=" O HIS D 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER D 470 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE D 380 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG D 458 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE D 464 " --> pdb=" O HIS D 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS D 456 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS D 466 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER D 426 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU D 421 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS D 428 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE D 419 " --> pdb=" O CYS D 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA D 430 " --> pdb=" O PRO D 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS E 466 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY E 376 " --> pdb=" O HIS E 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS E 468 " --> pdb=" O GLY E 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR E 378 " --> pdb=" O HIS E 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER E 470 " --> pdb=" O THR E 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE E 380 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG E 458 " --> pdb=" O TRP E 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE E 464 " --> pdb=" O HIS E 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS E 456 " --> pdb=" O ILE E 464 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS E 466 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER E 426 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU E 421 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS E 428 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE E 419 " --> pdb=" O CYS E 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA E 430 " --> pdb=" O PRO E 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS F 466 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY F 376 " --> pdb=" O HIS F 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS F 468 " --> pdb=" O GLY F 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR F 378 " --> pdb=" O HIS F 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER F 470 " --> pdb=" O THR F 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE F 380 " --> pdb=" O SER F 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG F 458 " --> pdb=" O TRP F 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE F 464 " --> pdb=" O HIS F 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS F 456 " --> pdb=" O ILE F 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS F 466 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER F 426 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU F 421 " --> pdb=" O SER F 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS F 428 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE F 419 " --> pdb=" O CYS F 428 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA F 430 " --> pdb=" O PRO F 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS G 466 " --> pdb=" O ASP G 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY G 376 " --> pdb=" O HIS G 466 " (cutoff:3.500A) removed outlier: 11.978A pdb=" N HIS G 468 " --> pdb=" O GLY G 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR G 378 " --> pdb=" O HIS G 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER G 470 " --> pdb=" O THR G 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE G 380 " --> pdb=" O SER G 470 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP G 462 " --> pdb=" O ARG G 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG G 458 " --> pdb=" O TRP G 462 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE G 464 " --> pdb=" O HIS G 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS G 456 " --> pdb=" O ILE G 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS G 466 " --> pdb=" O VAL G 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER G 426 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU G 421 " --> pdb=" O SER G 426 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS G 428 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE G 419 " --> pdb=" O CYS G 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA G 430 " --> pdb=" O PRO G 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS H 466 " --> pdb=" O ASP H 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY H 376 " --> pdb=" O HIS H 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS H 468 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR H 378 " --> pdb=" O HIS H 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER H 470 " --> pdb=" O THR H 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE H 380 " --> pdb=" O SER H 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP H 462 " --> pdb=" O ARG H 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG H 458 " --> pdb=" O TRP H 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE H 464 " --> pdb=" O HIS H 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS H 456 " --> pdb=" O ILE H 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS H 466 " --> pdb=" O VAL H 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER H 426 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU H 421 " --> pdb=" O SER H 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS H 428 " --> pdb=" O ILE H 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE H 419 " --> pdb=" O CYS H 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA H 430 " --> pdb=" O PRO H 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS I 466 " --> pdb=" O ASP I 374 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N GLY I 376 " --> pdb=" O HIS I 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS I 468 " --> pdb=" O GLY I 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR I 378 " --> pdb=" O HIS I 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER I 470 " --> pdb=" O THR I 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE I 380 " --> pdb=" O SER I 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP I 462 " --> pdb=" O ARG I 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG I 458 " --> pdb=" O TRP I 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE I 464 " --> pdb=" O HIS I 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS I 456 " --> pdb=" O ILE I 464 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS I 466 " --> pdb=" O VAL I 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER I 426 " --> pdb=" O LEU I 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU I 421 " --> pdb=" O SER I 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS I 428 " --> pdb=" O ILE I 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE I 419 " --> pdb=" O CYS I 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA I 430 " --> pdb=" O PRO I 417 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS J 466 " --> pdb=" O ASP J 374 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N GLY J 376 " --> pdb=" O HIS J 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS J 468 " --> pdb=" O GLY J 376 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N THR J 378 " --> pdb=" O HIS J 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER J 470 " --> pdb=" O THR J 378 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N PHE J 380 " --> pdb=" O SER J 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP J 462 " --> pdb=" O ARG J 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG J 458 " --> pdb=" O TRP J 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE J 464 " --> pdb=" O HIS J 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS J 456 " --> pdb=" O ILE J 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS J 466 " --> pdb=" O VAL J 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER J 426 " --> pdb=" O LEU J 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU J 421 " --> pdb=" O SER J 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS J 428 " --> pdb=" O ILE J 419 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE J 419 " --> pdb=" O CYS J 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA J 430 " --> pdb=" O PRO J 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS K 466 " --> pdb=" O ASP K 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY K 376 " --> pdb=" O HIS K 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS K 468 " --> pdb=" O GLY K 376 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N THR K 378 " --> pdb=" O HIS K 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER K 470 " --> pdb=" O THR K 378 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N PHE K 380 " --> pdb=" O SER K 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP K 462 " --> pdb=" O ARG K 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG K 458 " --> pdb=" O TRP K 462 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE K 464 " --> pdb=" O HIS K 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS K 456 " --> pdb=" O ILE K 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS K 466 " --> pdb=" O VAL K 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER K 426 " --> pdb=" O LEU K 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU K 421 " --> pdb=" O SER K 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS K 428 " --> pdb=" O ILE K 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE K 419 " --> pdb=" O CYS K 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA K 430 " --> pdb=" O PRO K 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS L 466 " --> pdb=" O ASP L 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY L 376 " --> pdb=" O HIS L 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS L 468 " --> pdb=" O GLY L 376 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N THR L 378 " --> pdb=" O HIS L 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER L 470 " --> pdb=" O THR L 378 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N PHE L 380 " --> pdb=" O SER L 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP L 462 " --> pdb=" O ARG L 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG L 458 " --> pdb=" O TRP L 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE L 464 " --> pdb=" O HIS L 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS L 456 " --> pdb=" O ILE L 464 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS L 466 " --> pdb=" O VAL L 454 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER L 426 " --> pdb=" O LEU L 421 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU L 421 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS L 428 " --> pdb=" O ILE L 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE L 419 " --> pdb=" O CYS L 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA L 430 " --> pdb=" O PRO L 417 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS M 466 " --> pdb=" O ASP M 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY M 376 " --> pdb=" O HIS M 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS M 468 " --> pdb=" O GLY M 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR M 378 " --> pdb=" O HIS M 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER M 470 " --> pdb=" O THR M 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE M 380 " --> pdb=" O SER M 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP M 462 " --> pdb=" O ARG M 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG M 458 " --> pdb=" O TRP M 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE M 464 " --> pdb=" O HIS M 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS M 456 " --> pdb=" O ILE M 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS M 466 " --> pdb=" O VAL M 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER M 426 " --> pdb=" O LEU M 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU M 421 " --> pdb=" O SER M 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS M 428 " --> pdb=" O ILE M 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE M 419 " --> pdb=" O CYS M 428 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA M 430 " --> pdb=" O PRO M 417 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS N 466 " --> pdb=" O ASP N 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY N 376 " --> pdb=" O HIS N 466 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N HIS N 468 " --> pdb=" O GLY N 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR N 378 " --> pdb=" O HIS N 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER N 470 " --> pdb=" O THR N 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE N 380 " --> pdb=" O SER N 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP N 462 " --> pdb=" O ARG N 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG N 458 " --> pdb=" O TRP N 462 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE N 464 " --> pdb=" O HIS N 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS N 456 " --> pdb=" O ILE N 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS N 466 " --> pdb=" O VAL N 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER N 426 " --> pdb=" O LEU N 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU N 421 " --> pdb=" O SER N 426 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS N 428 " --> pdb=" O ILE N 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE N 419 " --> pdb=" O CYS N 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA N 430 " --> pdb=" O PRO N 417 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 14686 1.12 - 1.30: 2559 1.30 - 1.47: 5381 1.47 - 1.64: 7614 1.64 - 1.81: 112 Bond restraints: 30352 Sorted by residual: bond pdb=" N THR L 413 " pdb=" H THR L 413 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" ND2 ASN J 406 " pdb="HD21 ASN J 406 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N GLU C 349 " pdb=" H GLU C 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NE2 HIS J 411 " pdb=" HE2 HIS J 411 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" ND2 ASN G 406 " pdb="HD21 ASN G 406 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 30347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 45432 2.44 - 4.88: 7237 4.88 - 7.32: 1851 7.32 - 9.76: 94 9.76 - 12.20: 28 Bond angle restraints: 54642 Sorted by residual: angle pdb=" CA HIS G 468 " pdb=" CB HIS G 468 " pdb=" CG HIS G 468 " ideal model delta sigma weight residual 113.80 119.31 -5.51 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA HIS I 468 " pdb=" CB HIS I 468 " pdb=" CG HIS I 468 " ideal model delta sigma weight residual 113.80 119.30 -5.50 1.00e+00 1.00e+00 3.03e+01 angle pdb=" CA HIS L 468 " pdb=" CB HIS L 468 " pdb=" CG HIS L 468 " ideal model delta sigma weight residual 113.80 119.29 -5.49 1.00e+00 1.00e+00 3.01e+01 angle pdb=" CA HIS D 468 " pdb=" CB HIS D 468 " pdb=" CG HIS D 468 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" CA HIS K 468 " pdb=" CB HIS K 468 " pdb=" CG HIS K 468 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 ... (remaining 54637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 12824 14.25 - 28.51: 896 28.51 - 42.76: 280 42.76 - 57.02: 154 57.02 - 71.27: 196 Dihedral angle restraints: 14350 sinusoidal: 7686 harmonic: 6664 Sorted by residual: dihedral pdb=" CA GLU G 425 " pdb=" C GLU G 425 " pdb=" N SER G 426 " pdb=" CA SER G 426 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU I 425 " pdb=" C GLU I 425 " pdb=" N SER I 426 " pdb=" CA SER I 426 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU B 425 " pdb=" C GLU B 425 " pdb=" N SER B 426 " pdb=" CA SER B 426 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 14347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 932 0.046 - 0.093: 764 0.093 - 0.139: 356 0.139 - 0.186: 132 0.186 - 0.232: 56 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA PHE I 467 " pdb=" N PHE I 467 " pdb=" C PHE I 467 " pdb=" CB PHE I 467 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PHE J 467 " pdb=" N PHE J 467 " pdb=" C PHE J 467 " pdb=" CB PHE J 467 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE A 467 " pdb=" N PHE A 467 " pdb=" C PHE A 467 " pdb=" CB PHE A 467 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2237 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 469 " 0.288 9.50e-02 1.11e+02 1.32e-01 1.96e+02 pdb=" NE ARG N 469 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG N 469 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG N 469 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG N 469 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG N 469 " -0.203 2.00e-02 2.50e+03 pdb="HH12 ARG N 469 " 0.130 2.00e-02 2.50e+03 pdb="HH21 ARG N 469 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG N 469 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 469 " -0.288 9.50e-02 1.11e+02 1.32e-01 1.95e+02 pdb=" NE ARG K 469 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG K 469 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG K 469 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG K 469 " 0.019 2.00e-02 2.50e+03 pdb="HH11 ARG K 469 " 0.203 2.00e-02 2.50e+03 pdb="HH12 ARG K 469 " -0.130 2.00e-02 2.50e+03 pdb="HH21 ARG K 469 " 0.043 2.00e-02 2.50e+03 pdb="HH22 ARG K 469 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 469 " -0.289 9.50e-02 1.11e+02 1.32e-01 1.95e+02 pdb=" NE ARG J 469 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG J 469 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG J 469 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG J 469 " 0.019 2.00e-02 2.50e+03 pdb="HH11 ARG J 469 " 0.203 2.00e-02 2.50e+03 pdb="HH12 ARG J 469 " -0.130 2.00e-02 2.50e+03 pdb="HH21 ARG J 469 " 0.044 2.00e-02 2.50e+03 pdb="HH22 ARG J 469 " 0.056 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2702 2.23 - 2.82: 54871 2.82 - 3.42: 81798 3.42 - 4.01: 110980 4.01 - 4.60: 161929 Nonbonded interactions: 412280 Sorted by model distance: nonbonded pdb=" HH TYR J 431 " pdb=" OE1 GLU J 451 " model vdw 1.641 2.450 nonbonded pdb=" HH TYR E 431 " pdb=" OE1 GLU E 451 " model vdw 1.642 2.450 nonbonded pdb=" HH TYR L 431 " pdb=" OE1 GLU L 451 " model vdw 1.642 2.450 nonbonded pdb=" HH TYR K 431 " pdb=" OE1 GLU K 451 " model vdw 1.642 2.450 nonbonded pdb=" HH TYR F 431 " pdb=" OE1 GLU F 451 " model vdw 1.642 2.450 ... (remaining 412275 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 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.170 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.240 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:5.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.013 0.037 15638 Z= 0.817 Angle : 1.786 6.818 21210 Z= 1.230 Chirality : 0.082 0.232 2240 Planarity : 0.016 0.092 2772 Dihedral : 12.962 71.272 5740 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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 aren not related in a simple way. whole: 1.34 (0.20), residues: 1848 helix: -1.28 (0.19), residues: 518 sheet: 3.90 (0.19), residues: 574 loop : 0.08 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG D 469 TYR 0.127 0.034 TYR C 398 PHE 0.030 0.011 PHE E 394 TRP 0.033 0.014 TRP A 403 HIS 0.016 0.004 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.01301 (15638) covalent geometry : angle 1.78604 (21210) hydrogen bonds : bond 0.17024 ( 714) hydrogen bonds : angle 6.80172 ( 2016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.692 Fit side-chains REVERT: B 352 LYS cc_start: 0.7860 (tttt) cc_final: 0.7575 (ttpt) REVERT: B 353 VAL cc_start: 0.8279 (p) cc_final: 0.7937 (m) REVERT: B 359 GLU cc_start: 0.8330 (tt0) cc_final: 0.8079 (tt0) REVERT: B 396 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7976 (ttm-80) REVERT: B 425 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7727 (mm-30) REVERT: A 352 LYS cc_start: 0.7993 (tttt) cc_final: 0.7636 (ttpt) REVERT: A 353 VAL cc_start: 0.8328 (p) cc_final: 0.8047 (m) REVERT: A 359 GLU cc_start: 0.8139 (tt0) cc_final: 0.7902 (tt0) REVERT: A 396 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7938 (ttm170) REVERT: A 398 TYR cc_start: 0.8091 (m-80) cc_final: 0.7871 (m-80) REVERT: A 425 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7745 (mm-30) REVERT: C 352 LYS cc_start: 0.7920 (tttt) cc_final: 0.7583 (ttpt) REVERT: C 353 VAL cc_start: 0.8267 (p) cc_final: 0.8006 (m) REVERT: C 359 GLU cc_start: 0.8278 (tt0) cc_final: 0.7996 (tt0) REVERT: C 396 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.8003 (ttm170) REVERT: C 398 TYR cc_start: 0.8138 (m-80) cc_final: 0.7899 (m-80) REVERT: C 425 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7741 (mm-30) REVERT: D 352 LYS cc_start: 0.7971 (tttt) cc_final: 0.7696 (tmmt) REVERT: D 353 VAL cc_start: 0.8303 (p) cc_final: 0.7992 (m) REVERT: D 359 GLU cc_start: 0.8219 (tt0) cc_final: 0.7982 (tt0) REVERT: D 396 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7958 (ttp-170) REVERT: D 425 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7842 (mm-30) REVERT: E 352 LYS cc_start: 0.7941 (tttt) cc_final: 0.7647 (ttpt) REVERT: E 353 VAL cc_start: 0.8244 (p) cc_final: 0.7977 (m) REVERT: E 359 GLU cc_start: 0.8357 (tt0) cc_final: 0.8085 (tt0) REVERT: E 396 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7965 (ttm-80) REVERT: E 398 TYR cc_start: 0.8149 (m-80) cc_final: 0.7910 (m-80) REVERT: E 425 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7895 (mm-30) REVERT: F 352 LYS cc_start: 0.7969 (tttt) cc_final: 0.7746 (ttpt) REVERT: F 353 VAL cc_start: 0.8132 (p) cc_final: 0.7842 (m) REVERT: F 359 GLU cc_start: 0.8210 (tt0) cc_final: 0.7947 (tt0) REVERT: F 396 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7947 (ttm-80) REVERT: F 425 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7808 (mm-30) REVERT: G 353 VAL cc_start: 0.8217 (p) cc_final: 0.7952 (m) REVERT: G 396 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7919 (ttm170) REVERT: G 425 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7775 (mm-30) REVERT: H 352 LYS cc_start: 0.7805 (tttt) cc_final: 0.7532 (ttpt) REVERT: H 353 VAL cc_start: 0.8279 (p) cc_final: 0.7943 (m) REVERT: H 359 GLU cc_start: 0.8350 (tt0) cc_final: 0.8100 (tt0) REVERT: H 396 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.8000 (ttm-80) REVERT: H 425 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7753 (mm-30) REVERT: I 352 LYS cc_start: 0.7947 (tttt) cc_final: 0.7634 (ttpt) REVERT: I 353 VAL cc_start: 0.8229 (p) cc_final: 0.7949 (m) REVERT: I 359 GLU cc_start: 0.8176 (tt0) cc_final: 0.7949 (tt0) REVERT: I 396 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7941 (ttm170) REVERT: I 398 TYR cc_start: 0.8081 (m-80) cc_final: 0.7838 (m-80) REVERT: I 425 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7758 (mm-30) REVERT: J 352 LYS cc_start: 0.8004 (tttt) cc_final: 0.7675 (ttpt) REVERT: J 353 VAL cc_start: 0.8229 (p) cc_final: 0.7972 (m) REVERT: J 359 GLU cc_start: 0.8316 (tt0) cc_final: 0.8053 (tt0) REVERT: J 396 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7954 (ttm170) REVERT: J 398 TYR cc_start: 0.8156 (m-80) cc_final: 0.7908 (m-80) REVERT: J 425 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7734 (mm-30) REVERT: K 352 LYS cc_start: 0.7995 (tttt) cc_final: 0.7711 (tmmt) REVERT: K 353 VAL cc_start: 0.8290 (p) cc_final: 0.7984 (m) REVERT: K 359 GLU cc_start: 0.8241 (tt0) cc_final: 0.8012 (tt0) REVERT: K 396 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7996 (ttp-170) REVERT: K 398 TYR cc_start: 0.8109 (m-80) cc_final: 0.7906 (m-80) REVERT: K 425 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7826 (mm-30) REVERT: L 352 LYS cc_start: 0.7938 (tttt) cc_final: 0.7638 (ttpt) REVERT: L 353 VAL cc_start: 0.8181 (p) cc_final: 0.7953 (m) REVERT: L 359 GLU cc_start: 0.8236 (tt0) cc_final: 0.7970 (tt0) REVERT: L 396 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7934 (ttm-80) REVERT: L 398 TYR cc_start: 0.8149 (m-80) cc_final: 0.7915 (m-80) REVERT: L 425 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7750 (mm-30) REVERT: M 352 LYS cc_start: 0.7972 (tttt) cc_final: 0.7607 (tmmt) REVERT: M 353 VAL cc_start: 0.8392 (p) cc_final: 0.8043 (m) REVERT: M 359 GLU cc_start: 0.8205 (tt0) cc_final: 0.7936 (tt0) REVERT: M 396 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.8086 (ttm170) REVERT: M 425 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7775 (mm-30) REVERT: N 352 LYS cc_start: 0.7824 (tttt) cc_final: 0.7605 (ttpt) REVERT: N 353 VAL cc_start: 0.8240 (p) cc_final: 0.7954 (m) REVERT: N 396 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7899 (ttm170) REVERT: N 425 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7798 (mm-30) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 1.5919 time to fit residues: 634.6308 Evaluate side-chains 314 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.174381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141441 restraints weight = 37798.069| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.97 r_work: 0.3367 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15638 Z= 0.155 Angle : 0.625 5.243 21210 Z= 0.355 Chirality : 0.045 0.126 2240 Planarity : 0.006 0.034 2772 Dihedral : 5.544 20.847 2058 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.59 % Allowed : 7.94 % Favored : 90.48 % 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 aren not related in a simple way. whole: 2.02 (0.21), residues: 1848 helix: 0.29 (0.24), residues: 532 sheet: 3.03 (0.19), residues: 658 loop : 0.50 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 457 TYR 0.012 0.002 TYR H 398 PHE 0.016 0.002 PHE K 467 TRP 0.010 0.002 TRP J 455 HIS 0.003 0.001 HIS L 478 Details of bonding type rmsd covalent geometry : bond 0.00305 (15638) covalent geometry : angle 0.62494 (21210) hydrogen bonds : bond 0.06068 ( 714) hydrogen bonds : angle 5.49897 ( 2016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7261 (tt0) cc_final: 0.7047 (tt0) REVERT: B 464 ILE cc_start: 0.8709 (mt) cc_final: 0.8311 (tt) REVERT: A 359 GLU cc_start: 0.7267 (tt0) cc_final: 0.7033 (tt0) REVERT: A 425 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7150 (mm-30) REVERT: C 352 LYS cc_start: 0.7653 (tttt) cc_final: 0.7433 (ttpt) REVERT: C 359 GLU cc_start: 0.7360 (tt0) cc_final: 0.7046 (tt0) REVERT: C 425 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7074 (mm-30) REVERT: C 464 ILE cc_start: 0.8659 (mp) cc_final: 0.8402 (tt) REVERT: D 359 GLU cc_start: 0.7266 (tt0) cc_final: 0.7005 (tt0) REVERT: D 396 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7577 (ttm-80) REVERT: D 425 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7185 (mm-30) REVERT: E 352 LYS cc_start: 0.7715 (tttt) cc_final: 0.7500 (ttpp) REVERT: E 464 ILE cc_start: 0.8751 (mp) cc_final: 0.8347 (tt) REVERT: F 359 GLU cc_start: 0.7276 (tt0) cc_final: 0.7058 (tt0) REVERT: H 359 GLU cc_start: 0.7253 (tt0) cc_final: 0.7041 (tt0) REVERT: H 425 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7070 (mm-30) REVERT: H 464 ILE cc_start: 0.8697 (mt) cc_final: 0.8300 (tt) REVERT: I 359 GLU cc_start: 0.7263 (tt0) cc_final: 0.7028 (tt0) REVERT: I 425 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7149 (mm-30) REVERT: J 352 LYS cc_start: 0.7590 (tttt) cc_final: 0.7378 (ttpt) REVERT: J 359 GLU cc_start: 0.7380 (tt0) cc_final: 0.7063 (tt0) REVERT: J 425 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7041 (mm-30) REVERT: J 464 ILE cc_start: 0.8685 (mp) cc_final: 0.8412 (tt) REVERT: K 359 GLU cc_start: 0.7208 (tt0) cc_final: 0.6946 (tt0) REVERT: K 396 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7561 (ttm-80) REVERT: K 425 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7214 (mm-30) REVERT: L 352 LYS cc_start: 0.7731 (tttt) cc_final: 0.7525 (ttpp) REVERT: L 425 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7177 (mm-30) REVERT: M 359 GLU cc_start: 0.7284 (tt0) cc_final: 0.7037 (tt0) REVERT: M 425 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7124 (mm-30) outliers start: 26 outliers final: 3 residues processed: 329 average time/residue: 1.6620 time to fit residues: 585.5509 Evaluate side-chains 293 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain K residue 402 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.170917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137663 restraints weight = 37939.872| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.01 r_work: 0.3284 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15638 Z= 0.198 Angle : 0.634 5.204 21210 Z= 0.349 Chirality : 0.046 0.130 2240 Planarity : 0.007 0.055 2772 Dihedral : 5.097 17.258 2058 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.38 % Allowed : 9.65 % Favored : 87.97 % 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 aren not related in a simple way. whole: 1.92 (0.21), residues: 1848 helix: 0.27 (0.24), residues: 532 sheet: 3.08 (0.19), residues: 686 loop : 0.11 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 457 TYR 0.011 0.003 TYR D 431 PHE 0.019 0.002 PHE D 467 TRP 0.008 0.002 TRP N 455 HIS 0.005 0.002 HIS G 395 Details of bonding type rmsd covalent geometry : bond 0.00448 (15638) covalent geometry : angle 0.63416 (21210) hydrogen bonds : bond 0.06027 ( 714) hydrogen bonds : angle 5.13801 ( 2016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 330 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7332 (tt0) cc_final: 0.7112 (tt0) REVERT: A 359 GLU cc_start: 0.7355 (tt0) cc_final: 0.7105 (tt0) REVERT: A 425 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7158 (mm-30) REVERT: C 352 LYS cc_start: 0.7526 (tttt) cc_final: 0.7280 (ttpt) REVERT: C 359 GLU cc_start: 0.7425 (tt0) cc_final: 0.7150 (tt0) REVERT: C 425 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7073 (mm-30) REVERT: D 359 GLU cc_start: 0.7395 (tt0) cc_final: 0.7109 (tt0) REVERT: D 396 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7555 (ttm-80) REVERT: D 425 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7214 (mm-30) REVERT: E 352 LYS cc_start: 0.7652 (tttt) cc_final: 0.7366 (ttpt) REVERT: F 359 GLU cc_start: 0.7454 (tt0) cc_final: 0.7197 (tt0) REVERT: H 359 GLU cc_start: 0.7319 (tt0) cc_final: 0.7096 (tt0) REVERT: I 359 GLU cc_start: 0.7373 (tt0) cc_final: 0.7134 (tt0) REVERT: I 425 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7176 (mm-30) REVERT: J 352 LYS cc_start: 0.7488 (tttt) cc_final: 0.7235 (ttpt) REVERT: J 359 GLU cc_start: 0.7462 (tt0) cc_final: 0.7180 (tt0) REVERT: J 425 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7046 (mm-30) REVERT: K 352 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7489 (tttp) REVERT: K 359 GLU cc_start: 0.7387 (tt0) cc_final: 0.7090 (tt0) REVERT: K 396 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7563 (ttm-80) REVERT: K 425 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7212 (mm-30) REVERT: L 352 LYS cc_start: 0.7636 (tttt) cc_final: 0.7349 (ttpt) REVERT: M 359 GLU cc_start: 0.7449 (tt0) cc_final: 0.7201 (tt0) outliers start: 39 outliers final: 15 residues processed: 336 average time/residue: 1.6623 time to fit residues: 599.1141 Evaluate side-chains 334 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 319 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 396 ARG Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 355 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 35 optimal weight: 0.0170 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.175967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143244 restraints weight = 37608.239| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.00 r_work: 0.3394 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15638 Z= 0.107 Angle : 0.513 4.515 21210 Z= 0.279 Chirality : 0.043 0.128 2240 Planarity : 0.006 0.064 2772 Dihedral : 4.644 17.723 2058 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.20 % Allowed : 10.13 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.21), residues: 1848 helix: 0.77 (0.24), residues: 518 sheet: 3.12 (0.20), residues: 686 loop : -0.04 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 457 TYR 0.007 0.001 TYR K 398 PHE 0.011 0.001 PHE D 467 TRP 0.006 0.001 TRP N 455 HIS 0.002 0.001 HIS I 395 Details of bonding type rmsd covalent geometry : bond 0.00237 (15638) covalent geometry : angle 0.51259 (21210) hydrogen bonds : bond 0.04359 ( 714) hydrogen bonds : angle 4.75928 ( 2016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 342 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7379 (tt0) cc_final: 0.7159 (tt0) REVERT: A 359 GLU cc_start: 0.7416 (tt0) cc_final: 0.7212 (tt0) REVERT: A 425 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7282 (mm-30) REVERT: A 451 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8787 (mt-10) REVERT: C 359 GLU cc_start: 0.7551 (tt0) cc_final: 0.7280 (tt0) REVERT: C 424 ASP cc_start: 0.7394 (m-30) cc_final: 0.7166 (m-30) REVERT: C 425 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7124 (mm-30) REVERT: D 359 GLU cc_start: 0.7467 (tt0) cc_final: 0.7205 (tt0) REVERT: D 396 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7600 (ttm-80) REVERT: D 425 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7225 (mm-30) REVERT: D 451 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8863 (mt-10) REVERT: E 352 LYS cc_start: 0.7607 (tttt) cc_final: 0.7334 (ttpt) REVERT: F 359 GLU cc_start: 0.7523 (tt0) cc_final: 0.7259 (tt0) REVERT: G 464 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8203 (mt) REVERT: H 359 GLU cc_start: 0.7408 (tt0) cc_final: 0.7181 (tt0) REVERT: I 359 GLU cc_start: 0.7477 (tt0) cc_final: 0.7267 (tt0) REVERT: I 425 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7249 (mm-30) REVERT: J 352 LYS cc_start: 0.7534 (tttt) cc_final: 0.7329 (ttpt) REVERT: J 359 GLU cc_start: 0.7541 (tt0) cc_final: 0.7268 (tt0) REVERT: J 424 ASP cc_start: 0.7374 (m-30) cc_final: 0.7156 (m-30) REVERT: J 425 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7126 (mm-30) REVERT: K 352 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7386 (tttp) REVERT: K 359 GLU cc_start: 0.7458 (tt0) cc_final: 0.7186 (tt0) REVERT: K 396 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: K 425 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7215 (mm-30) REVERT: K 451 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8853 (mt-10) REVERT: L 352 LYS cc_start: 0.7604 (tttt) cc_final: 0.7334 (ttpt) REVERT: M 359 GLU cc_start: 0.7487 (tt0) cc_final: 0.7239 (tt0) REVERT: N 464 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8199 (mt) outliers start: 36 outliers final: 21 residues processed: 354 average time/residue: 1.6502 time to fit residues: 628.1657 Evaluate side-chains 359 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 333 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 396 ARG Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 402 LEU Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 464 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 136 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 163 optimal weight: 0.0980 chunk 101 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN C 401 ASN G 401 ASN I 401 ASN J 401 ASN N 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.174258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141656 restraints weight = 37917.203| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.98 r_work: 0.3388 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15638 Z= 0.120 Angle : 0.515 4.568 21210 Z= 0.279 Chirality : 0.044 0.127 2240 Planarity : 0.006 0.068 2772 Dihedral : 4.500 17.403 2058 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.14 % Allowed : 12.52 % Favored : 85.35 % 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 aren not related in a simple way. whole: 2.11 (0.21), residues: 1848 helix: 0.65 (0.23), residues: 532 sheet: 2.81 (0.20), residues: 714 loop : 0.35 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 457 TYR 0.007 0.002 TYR K 398 PHE 0.014 0.002 PHE J 467 TRP 0.005 0.001 TRP G 455 HIS 0.003 0.001 HIS F 395 Details of bonding type rmsd covalent geometry : bond 0.00275 (15638) covalent geometry : angle 0.51521 (21210) hydrogen bonds : bond 0.04512 ( 714) hydrogen bonds : angle 4.65386 ( 2016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7396 (tt0) cc_final: 0.7176 (tt0) REVERT: A 359 GLU cc_start: 0.7445 (tt0) cc_final: 0.7226 (tt0) REVERT: A 425 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7274 (mm-30) REVERT: A 451 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8788 (mt-10) REVERT: C 359 GLU cc_start: 0.7544 (tt0) cc_final: 0.7275 (tt0) REVERT: C 425 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7121 (mm-30) REVERT: D 359 GLU cc_start: 0.7489 (tt0) cc_final: 0.7225 (tt0) REVERT: D 396 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7559 (ttm-80) REVERT: D 425 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7162 (mm-30) REVERT: D 451 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8901 (mt-10) REVERT: E 352 LYS cc_start: 0.7569 (tttt) cc_final: 0.7306 (ttpt) REVERT: F 359 GLU cc_start: 0.7514 (tt0) cc_final: 0.7274 (tt0) REVERT: H 359 GLU cc_start: 0.7414 (tt0) cc_final: 0.7188 (tt0) REVERT: I 359 GLU cc_start: 0.7465 (tt0) cc_final: 0.7246 (tt0) REVERT: I 425 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7270 (mm-30) REVERT: J 359 GLU cc_start: 0.7495 (tt0) cc_final: 0.7245 (tt0) REVERT: J 425 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7095 (mm-30) REVERT: K 352 LYS cc_start: 0.7889 (ttpp) cc_final: 0.7352 (tttp) REVERT: K 359 GLU cc_start: 0.7486 (tt0) cc_final: 0.7212 (tt0) REVERT: K 396 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7472 (ttm-80) REVERT: K 424 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7276 (m-30) REVERT: K 425 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7164 (mm-30) REVERT: K 451 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8898 (mt-10) REVERT: L 352 LYS cc_start: 0.7607 (tttt) cc_final: 0.7342 (ttpt) REVERT: M 359 GLU cc_start: 0.7502 (tt0) cc_final: 0.7263 (tt0) outliers start: 35 outliers final: 17 residues processed: 341 average time/residue: 1.7292 time to fit residues: 631.2702 Evaluate side-chains 347 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 326 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 30 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN D 401 ASN G 401 ASN I 401 ASN K 401 ASN N 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.174580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141561 restraints weight = 37698.800| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.99 r_work: 0.3289 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15638 Z= 0.214 Angle : 0.616 5.168 21210 Z= 0.338 Chirality : 0.046 0.130 2240 Planarity : 0.007 0.059 2772 Dihedral : 4.754 17.095 2058 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 13.13 % Favored : 84.74 % 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 aren not related in a simple way. whole: 1.95 (0.21), residues: 1848 helix: 0.54 (0.23), residues: 532 sheet: 2.77 (0.20), residues: 714 loop : 0.15 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 457 TYR 0.010 0.003 TYR B 398 PHE 0.020 0.003 PHE D 467 TRP 0.006 0.002 TRP J 455 HIS 0.004 0.001 HIS I 395 Details of bonding type rmsd covalent geometry : bond 0.00504 (15638) covalent geometry : angle 0.61617 (21210) hydrogen bonds : bond 0.05984 ( 714) hydrogen bonds : angle 4.90304 ( 2016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 327 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7479 (tt0) cc_final: 0.7230 (tt0) REVERT: B 451 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8895 (mt-10) REVERT: A 359 GLU cc_start: 0.7421 (tt0) cc_final: 0.7163 (tt0) REVERT: A 396 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7426 (ttp-110) REVERT: A 425 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7084 (mm-30) REVERT: A 451 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8873 (mt-10) REVERT: A 461 LYS cc_start: 0.7216 (ttpt) cc_final: 0.6940 (tmtt) REVERT: C 359 GLU cc_start: 0.7569 (tt0) cc_final: 0.7332 (tt0) REVERT: C 425 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7046 (mm-30) REVERT: D 352 LYS cc_start: 0.7824 (ttpp) cc_final: 0.7229 (tttm) REVERT: D 359 GLU cc_start: 0.7484 (tt0) cc_final: 0.7194 (tt0) REVERT: D 396 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7678 (ttm-80) REVERT: D 425 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7206 (mm-30) REVERT: D 451 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8901 (mt-10) REVERT: E 352 LYS cc_start: 0.7612 (tttt) cc_final: 0.7363 (ttpt) REVERT: F 359 GLU cc_start: 0.7606 (tt0) cc_final: 0.7379 (tt0) REVERT: F 396 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7553 (ttp-110) REVERT: H 359 GLU cc_start: 0.7433 (tt0) cc_final: 0.7180 (tt0) REVERT: H 451 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8887 (mt-10) REVERT: I 359 GLU cc_start: 0.7424 (tt0) cc_final: 0.7163 (tt0) REVERT: I 396 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7449 (ttp-110) REVERT: I 425 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7107 (mm-30) REVERT: I 461 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6958 (tmtt) REVERT: J 359 GLU cc_start: 0.7612 (tt0) cc_final: 0.7371 (tt0) REVERT: J 425 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7063 (mm-30) REVERT: K 352 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7340 (tttp) REVERT: K 359 GLU cc_start: 0.7482 (tt0) cc_final: 0.7189 (tt0) REVERT: K 396 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7631 (ttm-80) REVERT: K 425 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7217 (mm-30) REVERT: K 451 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8889 (mt-10) REVERT: L 352 LYS cc_start: 0.7588 (tttt) cc_final: 0.7349 (ttpt) REVERT: M 359 GLU cc_start: 0.7539 (tt0) cc_final: 0.7308 (tt0) REVERT: M 396 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7588 (ttp-110) outliers start: 35 outliers final: 20 residues processed: 340 average time/residue: 1.7894 time to fit residues: 650.8392 Evaluate side-chains 356 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 327 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 426 SER Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 396 ARG Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 0.0070 chunk 130 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN C 401 ASN G 401 ASN I 401 ASN J 401 ASN N 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.176128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143109 restraints weight = 37693.175| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.06 r_work: 0.3391 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15638 Z= 0.149 Angle : 0.556 4.816 21210 Z= 0.303 Chirality : 0.044 0.130 2240 Planarity : 0.006 0.058 2772 Dihedral : 4.612 17.457 2058 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.69 % Allowed : 13.19 % Favored : 84.13 % 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 aren not related in a simple way. whole: 2.00 (0.21), residues: 1848 helix: 0.67 (0.23), residues: 532 sheet: 2.77 (0.20), residues: 714 loop : 0.15 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 457 TYR 0.008 0.002 TYR K 398 PHE 0.015 0.002 PHE D 467 TRP 0.006 0.001 TRP C 455 HIS 0.003 0.001 HIS I 395 Details of bonding type rmsd covalent geometry : bond 0.00344 (15638) covalent geometry : angle 0.55591 (21210) hydrogen bonds : bond 0.05050 ( 714) hydrogen bonds : angle 4.78224 ( 2016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7445 (tt0) cc_final: 0.7201 (tt0) REVERT: B 425 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 359 GLU cc_start: 0.7362 (tt0) cc_final: 0.7122 (tt0) REVERT: A 396 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7330 (ttp-110) REVERT: A 425 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7036 (mm-30) REVERT: A 451 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8836 (mt-10) REVERT: A 461 LYS cc_start: 0.7148 (ttpt) cc_final: 0.6825 (tmtt) REVERT: C 359 GLU cc_start: 0.7520 (tt0) cc_final: 0.7282 (tt0) REVERT: C 425 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6996 (mm-30) REVERT: D 352 LYS cc_start: 0.7769 (ttpp) cc_final: 0.7168 (tttm) REVERT: D 359 GLU cc_start: 0.7451 (tt0) cc_final: 0.7166 (tt0) REVERT: D 396 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7594 (ttm-80) REVERT: D 425 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7162 (mm-30) REVERT: D 451 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8916 (mt-10) REVERT: E 352 LYS cc_start: 0.7499 (tttt) cc_final: 0.7229 (ttpt) REVERT: E 425 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7425 (mm-30) REVERT: F 359 GLU cc_start: 0.7548 (tt0) cc_final: 0.7262 (tt0) REVERT: H 359 GLU cc_start: 0.7441 (tt0) cc_final: 0.7200 (tt0) REVERT: I 359 GLU cc_start: 0.7362 (tt0) cc_final: 0.7117 (tt0) REVERT: I 396 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7349 (ttp-110) REVERT: I 425 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7069 (mm-30) REVERT: I 461 LYS cc_start: 0.7203 (ttpt) cc_final: 0.6887 (tmtt) REVERT: J 359 GLU cc_start: 0.7555 (tt0) cc_final: 0.7316 (tt0) REVERT: J 425 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6996 (mm-30) REVERT: K 352 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7219 (tttp) REVERT: K 359 GLU cc_start: 0.7462 (tt0) cc_final: 0.7170 (tt0) REVERT: K 396 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7533 (ttm-80) REVERT: K 425 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7153 (mm-30) REVERT: K 451 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8900 (mt-10) REVERT: L 352 LYS cc_start: 0.7458 (tttt) cc_final: 0.7198 (ttpt) REVERT: L 396 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7463 (ttp-110) REVERT: M 359 GLU cc_start: 0.7536 (tt0) cc_final: 0.7273 (tt0) outliers start: 44 outliers final: 22 residues processed: 342 average time/residue: 1.6946 time to fit residues: 621.1443 Evaluate side-chains 352 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 426 SER Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 396 ARG Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN G 401 ASN I 401 ASN N 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.139207 restraints weight = 37986.901| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.00 r_work: 0.3342 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15638 Z= 0.164 Angle : 0.570 4.899 21210 Z= 0.311 Chirality : 0.044 0.128 2240 Planarity : 0.007 0.090 2772 Dihedral : 4.638 17.379 2058 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 13.92 % Favored : 84.07 % 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 aren not related in a simple way. whole: 1.99 (0.21), residues: 1848 helix: 0.64 (0.23), residues: 532 sheet: 2.79 (0.20), residues: 714 loop : 0.12 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 457 TYR 0.009 0.003 TYR K 398 PHE 0.017 0.002 PHE K 467 TRP 0.006 0.001 TRP J 455 HIS 0.003 0.001 HIS I 395 Details of bonding type rmsd covalent geometry : bond 0.00385 (15638) covalent geometry : angle 0.57042 (21210) hydrogen bonds : bond 0.05267 ( 714) hydrogen bonds : angle 4.79540 ( 2016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 323 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 425 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 359 GLU cc_start: 0.7389 (tt0) cc_final: 0.7159 (tt0) REVERT: A 396 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7305 (ttp-110) REVERT: A 425 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7051 (mm-30) REVERT: A 451 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8814 (mt-10) REVERT: A 461 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6868 (tmtt) REVERT: C 359 GLU cc_start: 0.7554 (tt0) cc_final: 0.7305 (tt0) REVERT: C 425 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6942 (mm-30) REVERT: D 352 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7175 (tttm) REVERT: D 359 GLU cc_start: 0.7419 (tt0) cc_final: 0.7136 (tt0) REVERT: D 396 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7590 (ttm-80) REVERT: D 425 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7192 (mm-30) REVERT: D 451 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8908 (mt-10) REVERT: F 359 GLU cc_start: 0.7532 (tt0) cc_final: 0.7271 (tt0) REVERT: H 359 GLU cc_start: 0.7445 (tt0) cc_final: 0.7243 (tt0) REVERT: H 425 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7392 (mm-30) REVERT: I 359 GLU cc_start: 0.7432 (tt0) cc_final: 0.7192 (tt0) REVERT: I 396 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7313 (ttp-110) REVERT: I 425 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7038 (mm-30) REVERT: I 461 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6870 (tmtt) REVERT: J 359 GLU cc_start: 0.7547 (tt0) cc_final: 0.7297 (tt0) REVERT: J 425 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6946 (mm-30) REVERT: K 352 LYS cc_start: 0.7797 (ttpp) cc_final: 0.7258 (tttp) REVERT: K 359 GLU cc_start: 0.7419 (tt0) cc_final: 0.7134 (tt0) REVERT: K 396 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7548 (ttm-80) REVERT: K 425 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7184 (mm-30) REVERT: K 451 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8903 (mt-10) REVERT: L 461 LYS cc_start: 0.7288 (ttpt) cc_final: 0.7063 (tttm) REVERT: M 359 GLU cc_start: 0.7535 (tt0) cc_final: 0.7285 (tt0) outliers start: 33 outliers final: 23 residues processed: 334 average time/residue: 1.7076 time to fit residues: 611.1274 Evaluate side-chains 351 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 426 SER Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 167 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN G 401 ASN I 401 ASN N 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.139504 restraints weight = 37801.634| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.00 r_work: 0.3347 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15638 Z= 0.150 Angle : 0.561 4.951 21210 Z= 0.305 Chirality : 0.044 0.129 2240 Planarity : 0.007 0.088 2772 Dihedral : 4.608 17.483 2058 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.95 % Allowed : 14.71 % Favored : 83.33 % 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 aren not related in a simple way. whole: 2.00 (0.21), residues: 1848 helix: 0.87 (0.24), residues: 518 sheet: 2.81 (0.20), residues: 714 loop : -0.11 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 457 TYR 0.008 0.002 TYR K 398 PHE 0.015 0.002 PHE K 467 TRP 0.006 0.001 TRP J 455 HIS 0.003 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00349 (15638) covalent geometry : angle 0.56146 (21210) hydrogen bonds : bond 0.04997 ( 714) hydrogen bonds : angle 4.75689 ( 2016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 326 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 425 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 359 GLU cc_start: 0.7394 (tt0) cc_final: 0.7169 (tt0) REVERT: A 396 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7302 (ttp-110) REVERT: A 425 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7141 (mm-30) REVERT: A 451 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8823 (mt-10) REVERT: A 461 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6864 (tmtt) REVERT: C 359 GLU cc_start: 0.7535 (tt0) cc_final: 0.7288 (tt0) REVERT: C 425 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6928 (mm-30) REVERT: D 352 LYS cc_start: 0.7773 (ttpp) cc_final: 0.7187 (tttm) REVERT: D 359 GLU cc_start: 0.7413 (tt0) cc_final: 0.7125 (tt0) REVERT: D 396 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7600 (ttm-80) REVERT: D 425 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7201 (mm-30) REVERT: D 451 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8907 (mt-10) REVERT: E 424 ASP cc_start: 0.7286 (m-30) cc_final: 0.7062 (m-30) REVERT: E 425 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7302 (mm-30) REVERT: F 359 GLU cc_start: 0.7524 (tt0) cc_final: 0.7242 (tt0) REVERT: H 425 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7377 (mm-30) REVERT: I 359 GLU cc_start: 0.7441 (tt0) cc_final: 0.7207 (tt0) REVERT: I 396 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7309 (ttp-110) REVERT: I 425 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7138 (mm-30) REVERT: I 461 LYS cc_start: 0.7190 (ttpt) cc_final: 0.6892 (tmtt) REVERT: J 359 GLU cc_start: 0.7530 (tt0) cc_final: 0.7282 (tt0) REVERT: J 425 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6946 (mm-30) REVERT: K 352 LYS cc_start: 0.7770 (ttpp) cc_final: 0.7168 (tttm) REVERT: K 359 GLU cc_start: 0.7454 (tt0) cc_final: 0.7162 (tt0) REVERT: K 396 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7539 (ttm-80) REVERT: K 425 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7211 (mm-30) REVERT: K 451 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8909 (mt-10) REVERT: L 425 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7375 (mm-30) REVERT: L 461 LYS cc_start: 0.7293 (ttpt) cc_final: 0.7068 (tttm) REVERT: M 359 GLU cc_start: 0.7535 (tt0) cc_final: 0.7253 (tt0) outliers start: 32 outliers final: 24 residues processed: 336 average time/residue: 1.6832 time to fit residues: 605.1544 Evaluate side-chains 354 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 325 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 426 SER Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 396 ARG Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 0.0000 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN G 401 ASN I 401 ASN N 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.173378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140633 restraints weight = 37865.449| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.98 r_work: 0.3377 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15638 Z= 0.115 Angle : 0.514 5.059 21210 Z= 0.278 Chirality : 0.043 0.126 2240 Planarity : 0.007 0.090 2772 Dihedral : 4.417 17.813 2058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.65 % Allowed : 14.90 % Favored : 83.46 % 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 aren not related in a simple way. whole: 2.19 (0.21), residues: 1848 helix: 0.84 (0.24), residues: 532 sheet: 2.87 (0.21), residues: 714 loop : 0.24 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 457 TYR 0.007 0.002 TYR K 398 PHE 0.011 0.001 PHE C 467 TRP 0.007 0.001 TRP J 455 HIS 0.003 0.001 HIS I 395 Details of bonding type rmsd covalent geometry : bond 0.00263 (15638) covalent geometry : angle 0.51442 (21210) hydrogen bonds : bond 0.04221 ( 714) hydrogen bonds : angle 4.57743 ( 2016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 425 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 359 GLU cc_start: 0.7422 (tt0) cc_final: 0.7199 (tt0) REVERT: A 396 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7300 (ttp-110) REVERT: A 425 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7132 (mm-30) REVERT: A 451 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8797 (mt-10) REVERT: A 461 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6850 (tmtt) REVERT: C 359 GLU cc_start: 0.7481 (tt0) cc_final: 0.7201 (pt0) REVERT: C 425 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6898 (mm-30) REVERT: D 352 LYS cc_start: 0.7759 (ttpp) cc_final: 0.7161 (tttm) REVERT: D 396 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7588 (ttm-80) REVERT: D 424 ASP cc_start: 0.7367 (m-30) cc_final: 0.7154 (m-30) REVERT: D 425 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7150 (mm-30) REVERT: D 451 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8868 (mt-10) REVERT: E 359 GLU cc_start: 0.7441 (tt0) cc_final: 0.7171 (pt0) REVERT: E 424 ASP cc_start: 0.7309 (m-30) cc_final: 0.7067 (m-30) REVERT: E 425 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7276 (mm-30) REVERT: F 359 GLU cc_start: 0.7528 (tt0) cc_final: 0.7285 (pt0) REVERT: G 352 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7340 (tttp) REVERT: G 359 GLU cc_start: 0.7458 (tt0) cc_final: 0.7100 (pt0) REVERT: H 425 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7366 (mm-30) REVERT: I 359 GLU cc_start: 0.7465 (tt0) cc_final: 0.7231 (tt0) REVERT: I 396 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7298 (ttp-110) REVERT: I 425 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7115 (mm-30) REVERT: I 461 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6884 (tmtt) REVERT: J 359 GLU cc_start: 0.7468 (tt0) cc_final: 0.7182 (pt0) REVERT: J 425 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6909 (mm-30) REVERT: K 352 LYS cc_start: 0.7781 (ttpp) cc_final: 0.7174 (tttm) REVERT: K 359 GLU cc_start: 0.7446 (tt0) cc_final: 0.7164 (tt0) REVERT: K 396 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7516 (ttm-80) REVERT: K 424 ASP cc_start: 0.7416 (m-30) cc_final: 0.7180 (m-30) REVERT: K 425 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7208 (mm-30) REVERT: K 451 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8865 (mt-10) REVERT: L 359 GLU cc_start: 0.7442 (tt0) cc_final: 0.7155 (pt0) REVERT: L 425 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7361 (mm-30) REVERT: L 461 LYS cc_start: 0.7256 (ttpt) cc_final: 0.7038 (tttm) REVERT: M 359 GLU cc_start: 0.7539 (tt0) cc_final: 0.7315 (pt0) REVERT: N 359 GLU cc_start: 0.7466 (tt0) cc_final: 0.7095 (pt0) outliers start: 27 outliers final: 19 residues processed: 335 average time/residue: 1.6924 time to fit residues: 606.6268 Evaluate side-chains 348 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 324 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 426 SER Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 396 ARG Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN F 401 ASN I 401 ASN M 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.170533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137515 restraints weight = 38191.022| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.98 r_work: 0.3333 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15638 Z= 0.208 Angle : 0.614 5.022 21210 Z= 0.334 Chirality : 0.045 0.128 2240 Planarity : 0.008 0.087 2772 Dihedral : 4.682 17.328 2058 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 15.51 % Favored : 82.78 % 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 aren not related in a simple way. whole: 1.96 (0.21), residues: 1848 helix: 0.82 (0.23), residues: 518 sheet: 2.80 (0.20), residues: 714 loop : -0.16 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 457 TYR 0.010 0.003 TYR H 398 PHE 0.020 0.003 PHE L 467 TRP 0.006 0.002 TRP C 462 HIS 0.004 0.001 HIS M 468 Details of bonding type rmsd covalent geometry : bond 0.00492 (15638) covalent geometry : angle 0.61381 (21210) hydrogen bonds : bond 0.05724 ( 714) hydrogen bonds : angle 4.82408 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12137.93 seconds wall clock time: 205 minutes 26.48 seconds (12326.48 seconds total)