Starting phenix.real_space_refine on Tue May 27 15:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8syg_40873/05_2025/8syg_40873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syg_40873/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8syg_40873/05_2025/8syg_40873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syg_40873/05_2025/8syg_40873.map" model { file = "/net/cci-nas-00/data/ceres_data/8syg_40873/05_2025/8syg_40873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syg_40873/05_2025/8syg_40873.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29932 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, K, J, M, L, N Time building chain proxies: 7.94, per 1000 atoms: 0.27 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: 7.62 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.77 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: 11.02 Time building geometry restraints manager: 9.18 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' 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: 4.970 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: 0.480 Extract box with map and model: 1.180 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 55.360 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.140 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.014 TRP A 403 HIS 0.016 0.004 HIS A 456 PHE 0.030 0.011 PHE E 394 TYR 0.127 0.034 TYR C 398 ARG 0.008 0.002 ARG D 469 Details of bonding type rmsd hydrogen bonds : bond 0.17024 ( 714) hydrogen bonds : angle 6.80172 ( 2016) covalent geometry : bond 0.01301 (15638) covalent geometry : angle 1.78604 (21210) *********************** 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 : 2.654 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: 3.7077 time to fit residues: 1484.6863 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 : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.174587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141692 restraints weight = 37657.729| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.97 r_work: 0.3359 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2362 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= 0.155 Angle : 0.616 4.796 21210 Z= 0.346 Chirality : 0.044 0.126 2240 Planarity : 0.006 0.038 2772 Dihedral : 5.451 20.350 2058 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.21), residues: 1848 helix: 0.37 (0.24), residues: 532 sheet: 2.99 (0.19), residues: 686 loop : 0.38 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 455 HIS 0.004 0.001 HIS L 478 PHE 0.013 0.002 PHE K 467 TYR 0.011 0.002 TYR H 398 ARG 0.005 0.001 ARG I 457 Details of bonding type rmsd hydrogen bonds : bond 0.05789 ( 714) hydrogen bonds : angle 5.42592 ( 2016) covalent geometry : bond 0.00332 (15638) covalent geometry : angle 0.61575 (21210) *********************** 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 345 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 319 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7291 (tt0) cc_final: 0.7083 (tt0) REVERT: A 359 GLU cc_start: 0.7311 (tt0) cc_final: 0.7076 (tt0) REVERT: A 425 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7126 (mm-30) REVERT: C 352 LYS cc_start: 0.7679 (tttt) cc_final: 0.7469 (ttpt) REVERT: C 359 GLU cc_start: 0.7392 (tt0) cc_final: 0.7079 (tt0) REVERT: C 425 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7116 (mm-30) REVERT: C 464 ILE cc_start: 0.8657 (mp) cc_final: 0.8399 (tt) REVERT: D 359 GLU cc_start: 0.7293 (tt0) cc_final: 0.7033 (tt0) REVERT: D 396 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7584 (ttm-80) REVERT: D 425 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7210 (mm-30) REVERT: E 352 LYS cc_start: 0.7738 (tttt) cc_final: 0.7535 (ttpp) REVERT: F 359 GLU cc_start: 0.7320 (tt0) cc_final: 0.7051 (tt0) REVERT: H 359 GLU cc_start: 0.7278 (tt0) cc_final: 0.7068 (tt0) REVERT: I 359 GLU cc_start: 0.7272 (tt0) cc_final: 0.7046 (tt0) REVERT: I 425 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7178 (mm-30) REVERT: J 352 LYS cc_start: 0.7632 (tttt) cc_final: 0.7419 (ttpt) REVERT: J 359 GLU cc_start: 0.7387 (tt0) cc_final: 0.7071 (tt0) REVERT: J 425 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7092 (mm-30) REVERT: J 464 ILE cc_start: 0.8676 (mp) cc_final: 0.8403 (tt) REVERT: K 359 GLU cc_start: 0.7246 (tt0) cc_final: 0.6982 (tt0) REVERT: K 396 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7569 (ttm-80) REVERT: K 425 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7206 (mm-30) REVERT: M 359 GLU cc_start: 0.7314 (tt0) cc_final: 0.7050 (tt0) outliers start: 26 outliers final: 2 residues processed: 333 average time/residue: 3.6968 time to fit residues: 1322.1957 Evaluate side-chains 295 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 293 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 402 LEU 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 81 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.175913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143845 restraints weight = 37996.041| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.92 r_work: 0.3397 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15638 Z= 0.115 Angle : 0.533 4.071 21210 Z= 0.292 Chirality : 0.044 0.126 2240 Planarity : 0.006 0.052 2772 Dihedral : 4.843 17.445 2058 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.16 % Allowed : 11.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.21), residues: 1848 helix: 0.78 (0.24), residues: 518 sheet: 3.04 (0.19), residues: 686 loop : 0.00 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 455 HIS 0.003 0.001 HIS J 395 PHE 0.012 0.002 PHE J 467 TYR 0.008 0.002 TYR I 398 ARG 0.005 0.000 ARG G 457 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 714) hydrogen bonds : angle 4.95129 ( 2016) covalent geometry : bond 0.00248 (15638) covalent geometry : angle 0.53307 (21210) *********************** 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 346 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 327 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7339 (tt0) cc_final: 0.7110 (tt0) REVERT: C 359 GLU cc_start: 0.7442 (tt0) cc_final: 0.7157 (tt0) REVERT: D 359 GLU cc_start: 0.7358 (tt0) cc_final: 0.7075 (tt0) REVERT: D 396 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7562 (ttm-80) REVERT: D 425 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7210 (mm-30) REVERT: E 352 LYS cc_start: 0.7666 (tttt) cc_final: 0.7454 (ttpt) REVERT: F 359 GLU cc_start: 0.7424 (tt0) cc_final: 0.7176 (tt0) REVERT: H 359 GLU cc_start: 0.7375 (tt0) cc_final: 0.7143 (tt0) REVERT: I 359 GLU cc_start: 0.7408 (tt0) cc_final: 0.7206 (tt0) REVERT: J 359 GLU cc_start: 0.7446 (tt0) cc_final: 0.7175 (tt0) REVERT: J 425 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7158 (mm-30) REVERT: K 359 GLU cc_start: 0.7338 (tt0) cc_final: 0.7077 (tt0) REVERT: K 396 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7578 (ttm-80) REVERT: K 425 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7189 (mm-30) REVERT: M 359 GLU cc_start: 0.7384 (tt0) cc_final: 0.7142 (tt0) outliers start: 19 outliers final: 4 residues processed: 329 average time/residue: 3.8789 time to fit residues: 1369.7723 Evaluate side-chains 317 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 313 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.170693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137698 restraints weight = 38208.112| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.99 r_work: 0.3274 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15638 Z= 0.190 Angle : 0.614 4.841 21210 Z= 0.337 Chirality : 0.046 0.128 2240 Planarity : 0.007 0.067 2772 Dihedral : 4.878 17.199 2058 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.47 % Allowed : 11.84 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.21), residues: 1848 helix: 0.37 (0.23), residues: 532 sheet: 3.13 (0.20), residues: 686 loop : 0.04 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 455 HIS 0.006 0.002 HIS G 395 PHE 0.020 0.002 PHE K 467 TYR 0.010 0.003 TYR K 398 ARG 0.006 0.001 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.05873 ( 714) hydrogen bonds : angle 4.98286 ( 2016) covalent geometry : bond 0.00439 (15638) covalent geometry : angle 0.61387 (21210) *********************** 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 362 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 338 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7348 (tt0) cc_final: 0.7108 (tt0) REVERT: C 359 GLU cc_start: 0.7445 (tt0) cc_final: 0.7208 (tt0) REVERT: D 359 GLU cc_start: 0.7431 (tt0) cc_final: 0.7141 (tt0) REVERT: D 396 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7563 (ttm-80) REVERT: D 425 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7186 (mm-30) REVERT: E 352 LYS cc_start: 0.7598 (tttt) cc_final: 0.7333 (ttpt) REVERT: F 359 GLU cc_start: 0.7481 (tt0) cc_final: 0.7207 (tt0) REVERT: H 359 GLU cc_start: 0.7311 (tt0) cc_final: 0.7072 (tt0) REVERT: I 359 GLU cc_start: 0.7356 (tt0) cc_final: 0.7121 (tt0) REVERT: J 359 GLU cc_start: 0.7460 (tt0) cc_final: 0.7218 (tt0) REVERT: J 425 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7017 (mm-30) REVERT: K 359 GLU cc_start: 0.7392 (tt0) cc_final: 0.7108 (tt0) REVERT: K 396 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7565 (ttm-80) REVERT: K 425 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7193 (mm-30) REVERT: M 359 GLU cc_start: 0.7476 (tt0) cc_final: 0.7200 (tt0) outliers start: 24 outliers final: 11 residues processed: 346 average time/residue: 3.6855 time to fit residues: 1375.9434 Evaluate side-chains 342 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 331 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain D 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 402 LEU Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 402 LEU 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 169 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 146 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.172720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140109 restraints weight = 37975.201| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.97 r_work: 0.3304 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3425 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= 0.147 Angle : 0.550 4.570 21210 Z= 0.302 Chirality : 0.044 0.130 2240 Planarity : 0.006 0.060 2772 Dihedral : 4.655 17.334 2058 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.08 % Allowed : 12.64 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.21), residues: 1848 helix: 0.75 (0.24), residues: 518 sheet: 2.75 (0.20), residues: 714 loop : 0.05 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 455 HIS 0.004 0.001 HIS G 395 PHE 0.014 0.002 PHE D 467 TYR 0.008 0.002 TYR K 398 ARG 0.006 0.001 ARG M 457 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 714) hydrogen bonds : angle 4.82298 ( 2016) covalent geometry : bond 0.00339 (15638) covalent geometry : angle 0.55023 (21210) *********************** 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 367 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 333 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7410 (tt0) cc_final: 0.7165 (tt0) REVERT: A 451 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8850 (mt-10) REVERT: A 461 LYS cc_start: 0.7147 (ttpt) cc_final: 0.6839 (tmtt) REVERT: C 359 GLU cc_start: 0.7488 (tt0) cc_final: 0.7224 (tt0) REVERT: D 359 GLU cc_start: 0.7454 (tt0) cc_final: 0.7174 (tt0) REVERT: D 396 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7599 (ttm-80) REVERT: D 425 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7129 (mm-30) REVERT: D 451 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8909 (mt-10) REVERT: E 352 LYS cc_start: 0.7589 (tttt) cc_final: 0.7302 (ttpt) REVERT: F 359 GLU cc_start: 0.7482 (tt0) cc_final: 0.7226 (tt0) REVERT: H 359 GLU cc_start: 0.7429 (tt0) cc_final: 0.7174 (tt0) REVERT: I 359 GLU cc_start: 0.7434 (tt0) cc_final: 0.7219 (tt0) REVERT: I 451 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8808 (mt-10) REVERT: I 461 LYS cc_start: 0.7148 (ttpt) cc_final: 0.6851 (tmtt) REVERT: J 359 GLU cc_start: 0.7493 (tt0) cc_final: 0.7249 (tt0) REVERT: J 425 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7036 (mm-30) REVERT: K 359 GLU cc_start: 0.7471 (tt0) cc_final: 0.7186 (tt0) REVERT: K 396 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7573 (ttm-80) REVERT: K 425 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7152 (mm-30) REVERT: K 451 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8922 (mt-10) REVERT: M 359 GLU cc_start: 0.7476 (tt0) cc_final: 0.7217 (tt0) outliers start: 34 outliers final: 21 residues processed: 347 average time/residue: 3.6926 time to fit residues: 1377.2853 Evaluate side-chains 354 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 329 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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 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 402 LEU 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 I residue 451 GLU 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 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 45 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 ASN A 401 ASN D 401 ASN F 401 ASN G 401 ASN H 401 ASN I 401 ASN K 401 ASN M 401 ASN N 401 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.172124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140237 restraints weight = 38063.144| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.89 r_work: 0.3332 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3490 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= 0.148 Angle : 0.554 4.765 21210 Z= 0.302 Chirality : 0.044 0.128 2240 Planarity : 0.006 0.053 2772 Dihedral : 4.593 17.311 2058 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 13.68 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.21), residues: 1848 helix: 0.57 (0.23), residues: 532 sheet: 2.77 (0.20), residues: 714 loop : 0.21 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 455 HIS 0.003 0.001 HIS N 395 PHE 0.015 0.002 PHE D 467 TYR 0.008 0.002 TYR K 398 ARG 0.006 0.001 ARG N 457 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 714) hydrogen bonds : angle 4.77829 ( 2016) covalent geometry : bond 0.00345 (15638) covalent geometry : angle 0.55434 (21210) *********************** 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: 33 poor density : 329 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7458 (tt0) cc_final: 0.7205 (tt0) REVERT: A 451 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8820 (mt-10) REVERT: A 461 LYS cc_start: 0.7164 (ttpt) cc_final: 0.6869 (tmtt) REVERT: C 359 GLU cc_start: 0.7507 (tt0) cc_final: 0.7256 (tt0) REVERT: D 359 GLU cc_start: 0.7464 (tt0) cc_final: 0.7195 (tt0) REVERT: D 396 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7628 (ttm-80) REVERT: D 425 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7189 (mm-30) REVERT: D 451 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8874 (mt-10) REVERT: E 352 LYS cc_start: 0.7615 (tttt) cc_final: 0.7374 (ttpt) REVERT: F 359 GLU cc_start: 0.7565 (tt0) cc_final: 0.7303 (tt0) REVERT: H 359 GLU cc_start: 0.7459 (tt0) cc_final: 0.7205 (tt0) REVERT: I 359 GLU cc_start: 0.7424 (tt0) cc_final: 0.7186 (tt0) REVERT: I 451 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8840 (mt-10) REVERT: I 461 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6878 (tmtt) REVERT: J 359 GLU cc_start: 0.7520 (tt0) cc_final: 0.7272 (tt0) REVERT: J 425 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7010 (mm-30) REVERT: K 359 GLU cc_start: 0.7504 (tt0) cc_final: 0.7228 (tt0) REVERT: K 396 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7623 (ttm-80) REVERT: K 425 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7208 (mm-30) REVERT: K 451 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8884 (mt-10) REVERT: M 359 GLU cc_start: 0.7558 (tt0) cc_final: 0.7305 (tt0) outliers start: 33 outliers final: 20 residues processed: 341 average time/residue: 3.7869 time to fit residues: 1387.3957 Evaluate side-chains 352 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 328 time to evaluate : 2.284 ------------------------------------------------------------------------------- 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 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 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 I residue 402 LEU Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 451 GLU 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 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 8 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 ASN A 401 ASN D 401 ASN G 401 ASN H 401 ASN I 401 ASN K 401 ASN N 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.171552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138520 restraints weight = 38046.114| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.99 r_work: 0.3351 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15638 Z= 0.160 Angle : 0.566 4.801 21210 Z= 0.309 Chirality : 0.044 0.129 2240 Planarity : 0.006 0.061 2772 Dihedral : 4.599 17.279 2058 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.44 % Allowed : 13.80 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.21), residues: 1848 helix: 0.63 (0.23), residues: 532 sheet: 2.77 (0.20), residues: 714 loop : 0.19 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 455 HIS 0.003 0.001 HIS A 395 PHE 0.016 0.002 PHE D 467 TYR 0.008 0.002 TYR K 398 ARG 0.005 0.001 ARG N 457 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 714) hydrogen bonds : angle 4.79184 ( 2016) covalent geometry : bond 0.00372 (15638) covalent geometry : angle 0.56583 (21210) *********************** 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 369 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7476 (tt0) cc_final: 0.7242 (tt0) REVERT: A 396 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7318 (ttp-110) REVERT: A 425 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 451 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8827 (mt-10) REVERT: A 461 LYS cc_start: 0.7189 (ttpt) cc_final: 0.6861 (tmtt) REVERT: C 359 GLU cc_start: 0.7440 (tt0) cc_final: 0.7186 (tt0) REVERT: C 464 ILE cc_start: 0.8636 (mt) cc_final: 0.8241 (tt) REVERT: D 359 GLU cc_start: 0.7407 (tt0) cc_final: 0.7124 (tt0) REVERT: D 396 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7575 (ttm-80) REVERT: D 425 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7172 (mm-30) REVERT: D 451 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8892 (mt-10) REVERT: E 425 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7364 (mm-30) REVERT: F 359 GLU cc_start: 0.7535 (tt0) cc_final: 0.7269 (tt0) REVERT: F 396 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7544 (ttp-110) REVERT: H 359 GLU cc_start: 0.7472 (tt0) cc_final: 0.7237 (tt0) REVERT: I 359 GLU cc_start: 0.7412 (tt0) cc_final: 0.7177 (tt0) REVERT: I 396 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7360 (ttp-110) REVERT: I 425 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7271 (mm-30) REVERT: I 451 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8849 (mt-10) REVERT: I 461 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6885 (tmtt) REVERT: J 359 GLU cc_start: 0.7478 (tt0) cc_final: 0.7221 (tt0) REVERT: J 425 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6971 (mm-30) REVERT: J 464 ILE cc_start: 0.8632 (mt) cc_final: 0.8244 (tt) REVERT: K 359 GLU cc_start: 0.7443 (tt0) cc_final: 0.7145 (tt0) REVERT: K 396 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7599 (ttm-80) REVERT: K 425 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7166 (mm-30) REVERT: K 451 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8898 (mt-10) REVERT: L 461 LYS cc_start: 0.7217 (ttpt) cc_final: 0.7011 (tttm) REVERT: M 359 GLU cc_start: 0.7537 (tt0) cc_final: 0.7277 (tt0) REVERT: M 396 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7581 (ttp-110) outliers start: 40 outliers final: 21 residues processed: 342 average time/residue: 3.7962 time to fit residues: 1398.8912 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 : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 396 ARG Chi-restraints excluded: chain F residue 402 LEU 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 I residue 396 ARG Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 451 GLU 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 396 ARG Chi-restraints excluded: chain M residue 402 LEU 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 85 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 ASN A 401 ASN D 401 ASN G 401 ASN H 401 ASN I 401 ASN K 401 ASN N 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.171772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.138890 restraints weight = 38164.620| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.98 r_work: 0.3354 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15638 Z= 0.148 Angle : 0.554 4.905 21210 Z= 0.302 Chirality : 0.044 0.129 2240 Planarity : 0.007 0.088 2772 Dihedral : 4.560 17.352 2058 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.01 % Allowed : 14.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.21), residues: 1848 helix: 0.67 (0.23), residues: 532 sheet: 2.81 (0.20), residues: 714 loop : 0.14 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 455 HIS 0.003 0.001 HIS A 395 PHE 0.015 0.002 PHE D 467 TYR 0.007 0.002 TYR K 398 ARG 0.012 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 714) hydrogen bonds : angle 4.73690 ( 2016) covalent geometry : bond 0.00345 (15638) covalent geometry : angle 0.55415 (21210) *********************** 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 355 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 322 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7497 (tt0) cc_final: 0.7252 (tt0) REVERT: B 425 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 396 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7333 (ttp-110) REVERT: A 425 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 451 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8855 (mt-10) REVERT: A 461 LYS cc_start: 0.7170 (ttpt) cc_final: 0.6839 (tmtt) REVERT: C 359 GLU cc_start: 0.7487 (tt0) cc_final: 0.7233 (tt0) REVERT: C 464 ILE cc_start: 0.8647 (mt) cc_final: 0.8237 (tt) REVERT: D 352 LYS cc_start: 0.7775 (ttpp) cc_final: 0.7176 (tttm) REVERT: D 359 GLU cc_start: 0.7430 (tt0) cc_final: 0.7146 (tt0) REVERT: D 396 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7593 (ttm-80) REVERT: D 425 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7170 (mm-30) REVERT: D 451 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8882 (mt-10) REVERT: F 359 GLU cc_start: 0.7517 (tt0) cc_final: 0.7246 (tt0) REVERT: F 396 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7471 (ttp-110) REVERT: H 359 GLU cc_start: 0.7494 (tt0) cc_final: 0.7247 (tt0) REVERT: H 425 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7376 (mm-30) REVERT: I 359 GLU cc_start: 0.7387 (tt0) cc_final: 0.7162 (tt0) REVERT: I 396 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7335 (ttp-110) REVERT: I 425 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7250 (mm-30) REVERT: I 451 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8853 (mt-10) REVERT: I 461 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6863 (tmtt) REVERT: J 359 GLU cc_start: 0.7497 (tt0) cc_final: 0.7242 (tt0) REVERT: J 425 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6945 (mm-30) REVERT: J 464 ILE cc_start: 0.8642 (mt) cc_final: 0.8247 (tt) REVERT: K 352 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7167 (tttm) REVERT: K 359 GLU cc_start: 0.7438 (tt0) cc_final: 0.7148 (tt0) REVERT: K 396 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7591 (ttm-80) REVERT: K 425 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7200 (mm-30) REVERT: K 451 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8904 (mt-10) REVERT: L 425 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7425 (mm-30) REVERT: L 461 LYS cc_start: 0.7262 (ttpt) cc_final: 0.7034 (tttm) REVERT: M 359 GLU cc_start: 0.7507 (tt0) cc_final: 0.7236 (tt0) REVERT: M 396 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7549 (ttp-110) outliers start: 33 outliers final: 21 residues processed: 335 average time/residue: 3.8350 time to fit residues: 1379.4128 Evaluate side-chains 351 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 322 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 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 396 ARG Chi-restraints excluded: chain F residue 402 LEU 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 I residue 451 GLU 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 396 ARG Chi-restraints excluded: chain M residue 402 LEU 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 168 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 124 optimal weight: 0.0170 chunk 172 optimal weight: 0.0030 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 ASN A 401 ASN D 401 ASN G 401 ASN H 401 ASN I 401 ASN K 401 ASN N 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.172433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.139648 restraints weight = 38136.976| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.98 r_work: 0.3366 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3724 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= 0.131 Angle : 0.537 4.962 21210 Z= 0.291 Chirality : 0.044 0.128 2240 Planarity : 0.007 0.095 2772 Dihedral : 4.495 17.468 2058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.14 % Allowed : 14.90 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1848 helix: 0.74 (0.23), residues: 532 sheet: 2.85 (0.20), residues: 714 loop : 0.19 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 455 HIS 0.003 0.001 HIS I 395 PHE 0.013 0.002 PHE D 467 TYR 0.007 0.002 TYR K 398 ARG 0.016 0.001 ARG F 457 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 714) hydrogen bonds : angle 4.66650 ( 2016) covalent geometry : bond 0.00304 (15638) covalent geometry : angle 0.53742 (21210) *********************** 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 356 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7472 (tt0) cc_final: 0.7245 (tt0) REVERT: B 425 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 396 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7303 (ttp-110) REVERT: A 425 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 451 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8857 (mt-10) REVERT: A 461 LYS cc_start: 0.7164 (ttpt) cc_final: 0.6861 (tmtt) REVERT: C 359 GLU cc_start: 0.7468 (tt0) cc_final: 0.7230 (tt0) REVERT: D 352 LYS cc_start: 0.7774 (ttpp) cc_final: 0.7164 (tttm) REVERT: D 359 GLU cc_start: 0.7415 (tt0) cc_final: 0.7132 (tt0) REVERT: D 396 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7589 (ttm-80) REVERT: D 425 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7163 (mm-30) REVERT: D 451 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8876 (mt-10) REVERT: E 359 GLU cc_start: 0.7432 (tt0) cc_final: 0.7163 (pt0) REVERT: E 425 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7299 (mm-30) REVERT: F 359 GLU cc_start: 0.7519 (tt0) cc_final: 0.7282 (pt0) REVERT: F 396 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7476 (ttp-110) REVERT: H 359 GLU cc_start: 0.7450 (tt0) cc_final: 0.7219 (tt0) REVERT: H 425 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7338 (mm-30) REVERT: I 359 GLU cc_start: 0.7419 (tt0) cc_final: 0.7178 (tt0) REVERT: I 396 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7325 (ttp-110) REVERT: I 425 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7261 (mm-30) REVERT: I 451 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8863 (mt-10) REVERT: I 461 LYS cc_start: 0.7194 (ttpt) cc_final: 0.6885 (tmtt) REVERT: J 359 GLU cc_start: 0.7505 (tt0) cc_final: 0.7261 (tt0) REVERT: J 425 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6913 (mm-30) REVERT: K 359 GLU cc_start: 0.7434 (tt0) cc_final: 0.7150 (tt0) REVERT: K 396 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7526 (ttm-80) REVERT: K 425 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7194 (mm-30) REVERT: K 451 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8898 (mt-10) REVERT: L 425 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7389 (mm-30) REVERT: L 461 LYS cc_start: 0.7259 (ttpt) cc_final: 0.7038 (tttm) REVERT: M 352 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7380 (tttp) REVERT: M 359 GLU cc_start: 0.7523 (tt0) cc_final: 0.7295 (pt0) REVERT: M 396 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7561 (ttp-110) outliers start: 35 outliers final: 21 residues processed: 335 average time/residue: 3.8305 time to fit residues: 1378.3516 Evaluate side-chains 349 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 320 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 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 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 I residue 451 GLU 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 396 ARG Chi-restraints excluded: chain M residue 402 LEU 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 66 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 111 optimal weight: 0.0070 chunk 153 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 ASN A 401 ASN G 401 ASN H 401 ASN I 401 ASN K 401 ASN N 401 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.174546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141987 restraints weight = 38093.547| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.97 r_work: 0.3382 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15638 Z= 0.098 Angle : 0.499 5.034 21210 Z= 0.267 Chirality : 0.043 0.126 2240 Planarity : 0.007 0.094 2772 Dihedral : 4.296 17.752 2058 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.59 % Allowed : 15.20 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1848 helix: 1.10 (0.24), residues: 518 sheet: 2.89 (0.21), residues: 714 loop : 0.14 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 455 HIS 0.002 0.001 HIS H 395 PHE 0.010 0.001 PHE J 467 TYR 0.005 0.001 TYR M 398 ARG 0.015 0.001 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 714) hydrogen bonds : angle 4.48392 ( 2016) covalent geometry : bond 0.00222 (15638) covalent geometry : angle 0.49922 (21210) ********************** 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 341 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 GLU cc_start: 0.7423 (tt0) cc_final: 0.7156 (tt0) REVERT: B 425 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7266 (mm-30) REVERT: A 425 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 451 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8785 (mt-10) REVERT: A 461 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6836 (tmtt) REVERT: C 359 GLU cc_start: 0.7513 (tt0) cc_final: 0.7256 (tt0) REVERT: D 352 LYS cc_start: 0.7731 (ttpp) cc_final: 0.7201 (tttp) REVERT: D 396 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7594 (ttm-80) REVERT: D 424 ASP cc_start: 0.7383 (m-30) cc_final: 0.7148 (m-30) REVERT: D 425 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7158 (mm-30) REVERT: D 451 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8819 (mt-10) REVERT: E 359 GLU cc_start: 0.7467 (tt0) cc_final: 0.7165 (pt0) REVERT: F 359 GLU cc_start: 0.7531 (tt0) cc_final: 0.7288 (pt0) REVERT: F 396 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7502 (ttp-110) REVERT: G 352 LYS cc_start: 0.7758 (ttpp) cc_final: 0.7307 (tttp) REVERT: G 359 GLU cc_start: 0.7485 (tt0) cc_final: 0.7100 (pt0) REVERT: H 359 GLU cc_start: 0.7406 (tt0) cc_final: 0.7135 (tt0) REVERT: H 425 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7279 (mm-30) REVERT: I 359 GLU cc_start: 0.7501 (tt0) cc_final: 0.7260 (tt0) REVERT: I 425 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7223 (mm-30) REVERT: I 451 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8785 (mt-10) REVERT: I 461 LYS cc_start: 0.7153 (ttpt) cc_final: 0.6846 (tmtt) REVERT: J 359 GLU cc_start: 0.7500 (tt0) cc_final: 0.7242 (tt0) REVERT: J 425 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6897 (mm-30) REVERT: K 359 GLU cc_start: 0.7480 (tt0) cc_final: 0.7190 (tt0) REVERT: K 396 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7540 (ttm-80) REVERT: K 424 ASP cc_start: 0.7389 (m-30) cc_final: 0.7161 (m-30) REVERT: K 425 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7164 (mm-30) REVERT: K 451 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8832 (mt-10) REVERT: L 359 GLU cc_start: 0.7429 (tt0) cc_final: 0.7097 (pt0) REVERT: L 425 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7352 (mm-30) REVERT: L 461 LYS cc_start: 0.7219 (ttpt) cc_final: 0.7006 (tttm) REVERT: M 352 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7356 (tttp) REVERT: M 359 GLU cc_start: 0.7528 (tt0) cc_final: 0.7308 (pt0) REVERT: M 396 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7533 (ttp-110) REVERT: N 352 LYS cc_start: 0.7778 (ttpp) cc_final: 0.7304 (tttp) REVERT: N 359 GLU cc_start: 0.7471 (tt0) cc_final: 0.7076 (pt0) outliers start: 26 outliers final: 14 residues processed: 323 average time/residue: 4.0593 time to fit residues: 1409.3925 Evaluate side-chains 332 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 312 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 451 GLU 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 424 ASP Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain H residue 426 SER Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 451 GLU 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 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 31 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 chunk 38 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.5140 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.175645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142981 restraints weight = 38059.885| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.98 r_work: 0.3397 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15638 Z= 0.094 Angle : 0.486 4.878 21210 Z= 0.258 Chirality : 0.043 0.125 2240 Planarity : 0.007 0.089 2772 Dihedral : 4.156 18.192 2058 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.10 % Allowed : 15.93 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.21), residues: 1848 helix: 1.01 (0.23), residues: 532 sheet: 2.90 (0.21), residues: 714 loop : 0.50 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 455 HIS 0.002 0.000 HIS B 395 PHE 0.010 0.001 PHE F 467 TYR 0.008 0.001 TYR B 398 ARG 0.013 0.001 ARG I 457 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 714) hydrogen bonds : angle 4.35893 ( 2016) covalent geometry : bond 0.00218 (15638) covalent geometry : angle 0.48622 (21210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27005.96 seconds wall clock time: 461 minutes 11.53 seconds (27671.53 seconds total)