Starting phenix.real_space_refine on Mon Aug 25 16:24:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t17_40956/08_2025/8t17_40956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t17_40956/08_2025/8t17_40956.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/8t17_40956/08_2025/8t17_40956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t17_40956/08_2025/8t17_40956.map" model { file = "/net/cci-nas-00/data/ceres_data/8t17_40956/08_2025/8t17_40956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t17_40956/08_2025/8t17_40956.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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 56 5.16 5 C 9506 2.51 5 N 2688 2.21 5 O 2842 1.98 5 H 14462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29554 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2111 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N Time building chain proxies: 2.88, per 1000 atoms: 0.10 Number of scatterers: 29554 At special positions: 0 Unit cell: (137.408, 133.951, 73.457, 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 56 16.00 O 2842 8.00 N 2688 7.00 C 9506 6.00 H 14462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 674.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 14 sheets defined 35.6% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 408 through 428 removed outlier: 3.674A pdb=" N GLN A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU A 449 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'B' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU B 449 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 Processing helix chain 'C' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 449 removed outlier: 3.670A pdb=" N LEU C 449 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 525 Processing helix chain 'D' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 449 removed outlier: 3.670A pdb=" N LEU D 449 " --> pdb=" O PRO D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 525 Processing helix chain 'E' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU E 449 " --> pdb=" O PRO E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR E 462 " --> pdb=" O PHE E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 525 Processing helix chain 'F' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 449 removed outlier: 3.672A pdb=" N LEU F 449 " --> pdb=" O PRO F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR F 462 " --> pdb=" O PHE F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 525 Processing helix chain 'G' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU G 413 " --> pdb=" O ALA G 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE G 414 " --> pdb=" O ARG G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS G 435 " --> pdb=" O GLU G 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE G 436 " --> pdb=" O ALA G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU G 449 " --> pdb=" O PRO G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE G 461 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR G 462 " --> pdb=" O PHE G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 525 Processing helix chain 'H' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU H 413 " --> pdb=" O ALA H 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE H 414 " --> pdb=" O ARG H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS H 435 " --> pdb=" O GLU H 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE H 436 " --> pdb=" O ALA H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU H 449 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE H 461 " --> pdb=" O ASP H 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR H 462 " --> pdb=" O PHE H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 525 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU I 413 " --> pdb=" O ALA I 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE I 414 " --> pdb=" O ARG I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS I 435 " --> pdb=" O GLU I 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE I 436 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU I 449 " --> pdb=" O PRO I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE I 461 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR I 462 " --> pdb=" O PHE I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 525 Processing helix chain 'J' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU J 413 " --> pdb=" O ALA J 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE J 414 " --> pdb=" O ARG J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS J 435 " --> pdb=" O GLU J 431 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE J 436 " --> pdb=" O ALA J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU J 449 " --> pdb=" O PRO J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE J 461 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR J 462 " --> pdb=" O PHE J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 522 through 525 Processing helix chain 'K' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU K 413 " --> pdb=" O ALA K 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE K 414 " --> pdb=" O ARG K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS K 435 " --> pdb=" O GLU K 431 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE K 436 " --> pdb=" O ALA K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 449 removed outlier: 3.670A pdb=" N LEU K 449 " --> pdb=" O PRO K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR K 462 " --> pdb=" O PHE K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 522 through 525 Processing helix chain 'L' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU L 413 " --> pdb=" O ALA L 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE L 414 " --> pdb=" O ARG L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS L 435 " --> pdb=" O GLU L 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE L 436 " --> pdb=" O ALA L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.671A pdb=" N LEU L 449 " --> pdb=" O PRO L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE L 461 " --> pdb=" O ASP L 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR L 462 " --> pdb=" O PHE L 458 " (cutoff:3.500A) Processing helix chain 'L' and resid 522 through 525 Processing helix chain 'M' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU M 413 " --> pdb=" O ALA M 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE M 414 " --> pdb=" O ARG M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS M 435 " --> pdb=" O GLU M 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE M 436 " --> pdb=" O ALA M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 449 removed outlier: 3.672A pdb=" N LEU M 449 " --> pdb=" O PRO M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE M 461 " --> pdb=" O ASP M 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR M 462 " --> pdb=" O PHE M 458 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 525 Processing helix chain 'N' and resid 409 through 428 removed outlier: 3.608A pdb=" N GLU N 413 " --> pdb=" O ALA N 409 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE N 414 " --> pdb=" O ARG N 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 436 removed outlier: 3.872A pdb=" N LYS N 435 " --> pdb=" O GLU N 431 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE N 436 " --> pdb=" O ALA N 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 449 removed outlier: 3.670A pdb=" N LEU N 449 " --> pdb=" O PRO N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 456 through 466 removed outlier: 3.813A pdb=" N PHE N 461 " --> pdb=" O ASP N 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR N 462 " --> pdb=" O PHE N 458 " (cutoff:3.500A) Processing helix chain 'N' and resid 522 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS A 530 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY A 440 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS A 532 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR A 442 " --> pdb=" O HIS A 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER A 534 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE A 444 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 518 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A 531 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 516 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS A 533 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU A 514 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY A 535 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN A 512 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA A 490 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL A 485 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 492 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL A 483 " --> pdb=" O CYS A 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 494 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS B 530 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY B 440 " --> pdb=" O HIS B 530 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N HIS B 532 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR B 442 " --> pdb=" O HIS B 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER B 534 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE B 444 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 518 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 531 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR B 516 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS B 533 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU B 514 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 535 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN B 512 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA B 490 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL B 485 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS B 492 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 483 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 494 " --> pdb=" O PRO B 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS C 530 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY C 440 " --> pdb=" O HIS C 530 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N HIS C 532 " --> pdb=" O GLY C 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR C 442 " --> pdb=" O HIS C 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER C 534 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE C 444 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 518 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE C 531 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 516 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS C 533 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU C 514 " --> pdb=" O CYS C 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY C 535 " --> pdb=" O GLN C 512 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN C 512 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA C 490 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL C 485 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS C 492 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 483 " --> pdb=" O CYS C 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA C 494 " --> pdb=" O PRO C 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 453 through 454 removed outlier: 7.536A pdb=" N HIS D 530 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY D 440 " --> pdb=" O HIS D 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS D 532 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR D 442 " --> pdb=" O HIS D 532 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N SER D 534 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE D 444 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL D 518 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE D 531 " --> pdb=" O THR D 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR D 516 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS D 533 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU D 514 " --> pdb=" O CYS D 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY D 535 " --> pdb=" O GLN D 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN D 512 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA D 490 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL D 485 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS D 492 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 483 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA D 494 " --> pdb=" O PRO D 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS E 530 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N GLY E 440 " --> pdb=" O HIS E 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS E 532 " --> pdb=" O GLY E 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR E 442 " --> pdb=" O HIS E 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER E 534 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE E 444 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 518 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE E 531 " --> pdb=" O THR E 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR E 516 " --> pdb=" O PHE E 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS E 533 " --> pdb=" O GLU E 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU E 514 " --> pdb=" O CYS E 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY E 535 " --> pdb=" O GLN E 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN E 512 " --> pdb=" O GLY E 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA E 490 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL E 485 " --> pdb=" O ALA E 490 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS E 492 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL E 483 " --> pdb=" O CYS E 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA E 494 " --> pdb=" O PRO E 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 453 through 454 removed outlier: 7.536A pdb=" N HIS F 530 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY F 440 " --> pdb=" O HIS F 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS F 532 " --> pdb=" O GLY F 440 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR F 442 " --> pdb=" O HIS F 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER F 534 " --> pdb=" O THR F 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE F 444 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL F 518 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE F 531 " --> pdb=" O THR F 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR F 516 " --> pdb=" O PHE F 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS F 533 " --> pdb=" O GLU F 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU F 514 " --> pdb=" O CYS F 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY F 535 " --> pdb=" O GLN F 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN F 512 " --> pdb=" O GLY F 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA F 490 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL F 485 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS F 492 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL F 483 " --> pdb=" O CYS F 492 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA F 494 " --> pdb=" O PRO F 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS G 530 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY G 440 " --> pdb=" O HIS G 530 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N HIS G 532 " --> pdb=" O GLY G 440 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N THR G 442 " --> pdb=" O HIS G 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER G 534 " --> pdb=" O THR G 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE G 444 " --> pdb=" O SER G 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL G 518 " --> pdb=" O VAL G 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE G 531 " --> pdb=" O THR G 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR G 516 " --> pdb=" O PHE G 531 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS G 533 " --> pdb=" O GLU G 514 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU G 514 " --> pdb=" O CYS G 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY G 535 " --> pdb=" O GLN G 512 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 512 " --> pdb=" O GLY G 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA G 490 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL G 485 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS G 492 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL G 483 " --> pdb=" O CYS G 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA G 494 " --> pdb=" O PRO G 481 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS H 530 " --> pdb=" O ASP H 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY H 440 " --> pdb=" O HIS H 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS H 532 " --> pdb=" O GLY H 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR H 442 " --> pdb=" O HIS H 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER H 534 " --> pdb=" O THR H 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE H 444 " --> pdb=" O SER H 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL H 518 " --> pdb=" O VAL H 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE H 531 " --> pdb=" O THR H 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR H 516 " --> pdb=" O PHE H 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS H 533 " --> pdb=" O GLU H 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU H 514 " --> pdb=" O CYS H 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY H 535 " --> pdb=" O GLN H 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN H 512 " --> pdb=" O GLY H 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA H 490 " --> pdb=" O VAL H 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL H 485 " --> pdb=" O ALA H 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS H 492 " --> pdb=" O VAL H 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL H 483 " --> pdb=" O CYS H 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA H 494 " --> pdb=" O PRO H 481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS I 530 " --> pdb=" O ASP I 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY I 440 " --> pdb=" O HIS I 530 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N HIS I 532 " --> pdb=" O GLY I 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR I 442 " --> pdb=" O HIS I 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER I 534 " --> pdb=" O THR I 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE I 444 " --> pdb=" O SER I 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL I 518 " --> pdb=" O VAL I 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE I 531 " --> pdb=" O THR I 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR I 516 " --> pdb=" O PHE I 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS I 533 " --> pdb=" O GLU I 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU I 514 " --> pdb=" O CYS I 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY I 535 " --> pdb=" O GLN I 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN I 512 " --> pdb=" O GLY I 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA I 490 " --> pdb=" O VAL I 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL I 485 " --> pdb=" O ALA I 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS I 492 " --> pdb=" O VAL I 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL I 483 " --> pdb=" O CYS I 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA I 494 " --> pdb=" O PRO I 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS J 530 " --> pdb=" O ASP J 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY J 440 " --> pdb=" O HIS J 530 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N HIS J 532 " --> pdb=" O GLY J 440 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N THR J 442 " --> pdb=" O HIS J 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER J 534 " --> pdb=" O THR J 442 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N PHE J 444 " --> pdb=" O SER J 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL J 518 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE J 531 " --> pdb=" O THR J 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR J 516 " --> pdb=" O PHE J 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS J 533 " --> pdb=" O GLU J 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU J 514 " --> pdb=" O CYS J 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY J 535 " --> pdb=" O GLN J 512 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN J 512 " --> pdb=" O GLY J 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA J 490 " --> pdb=" O VAL J 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL J 485 " --> pdb=" O ALA J 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS J 492 " --> pdb=" O VAL J 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL J 483 " --> pdb=" O CYS J 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA J 494 " --> pdb=" O PRO J 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS K 530 " --> pdb=" O ASP K 438 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N GLY K 440 " --> pdb=" O HIS K 530 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N HIS K 532 " --> pdb=" O GLY K 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR K 442 " --> pdb=" O HIS K 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER K 534 " --> pdb=" O THR K 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE K 444 " --> pdb=" O SER K 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL K 518 " --> pdb=" O VAL K 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE K 531 " --> pdb=" O THR K 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR K 516 " --> pdb=" O PHE K 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS K 533 " --> pdb=" O GLU K 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU K 514 " --> pdb=" O CYS K 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY K 535 " --> pdb=" O GLN K 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN K 512 " --> pdb=" O GLY K 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA K 490 " --> pdb=" O VAL K 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL K 485 " --> pdb=" O ALA K 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS K 492 " --> pdb=" O VAL K 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL K 483 " --> pdb=" O CYS K 492 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA K 494 " --> pdb=" O PRO K 481 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS L 530 " --> pdb=" O ASP L 438 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N GLY L 440 " --> pdb=" O HIS L 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS L 532 " --> pdb=" O GLY L 440 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR L 442 " --> pdb=" O HIS L 532 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N SER L 534 " --> pdb=" O THR L 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE L 444 " --> pdb=" O SER L 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL L 518 " --> pdb=" O VAL L 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE L 531 " --> pdb=" O THR L 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR L 516 " --> pdb=" O PHE L 531 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS L 533 " --> pdb=" O GLU L 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU L 514 " --> pdb=" O CYS L 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY L 535 " --> pdb=" O GLN L 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN L 512 " --> pdb=" O GLY L 535 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA L 490 " --> pdb=" O VAL L 485 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL L 485 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS L 492 " --> pdb=" O VAL L 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL L 483 " --> pdb=" O CYS L 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA L 494 " --> pdb=" O PRO L 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 453 through 454 removed outlier: 7.536A pdb=" N HIS M 530 " --> pdb=" O ASP M 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY M 440 " --> pdb=" O HIS M 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS M 532 " --> pdb=" O GLY M 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR M 442 " --> pdb=" O HIS M 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER M 534 " --> pdb=" O THR M 442 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N PHE M 444 " --> pdb=" O SER M 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL M 518 " --> pdb=" O VAL M 529 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE M 531 " --> pdb=" O THR M 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR M 516 " --> pdb=" O PHE M 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS M 533 " --> pdb=" O GLU M 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU M 514 " --> pdb=" O CYS M 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY M 535 " --> pdb=" O GLN M 512 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN M 512 " --> pdb=" O GLY M 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA M 490 " --> pdb=" O VAL M 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL M 485 " --> pdb=" O ALA M 490 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS M 492 " --> pdb=" O VAL M 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL M 483 " --> pdb=" O CYS M 492 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA M 494 " --> pdb=" O PRO M 481 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 453 through 454 removed outlier: 7.535A pdb=" N HIS N 530 " --> pdb=" O ASP N 438 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N GLY N 440 " --> pdb=" O HIS N 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS N 532 " --> pdb=" O GLY N 440 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N THR N 442 " --> pdb=" O HIS N 532 " (cutoff:3.500A) removed outlier: 12.042A pdb=" N SER N 534 " --> pdb=" O THR N 442 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N PHE N 444 " --> pdb=" O SER N 534 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL N 518 " --> pdb=" O VAL N 529 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE N 531 " --> pdb=" O THR N 516 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR N 516 " --> pdb=" O PHE N 531 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS N 533 " --> pdb=" O GLU N 514 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU N 514 " --> pdb=" O CYS N 533 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY N 535 " --> pdb=" O GLN N 512 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN N 512 " --> pdb=" O GLY N 535 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA N 490 " --> pdb=" O VAL N 485 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL N 485 " --> pdb=" O ALA N 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS N 492 " --> pdb=" O VAL N 483 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL N 483 " --> pdb=" O CYS N 492 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA N 494 " --> pdb=" O PRO N 481 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 2.70 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: 14420 1.12 - 1.30: 2615 1.30 - 1.47: 5262 1.47 - 1.64: 7579 1.64 - 1.81: 70 Bond restraints: 29946 Sorted by residual: bond pdb=" CE3 TRP B 519 " pdb=" HE3 TRP B 519 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE I 496 " pdb=" H ILE I 496 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE B 496 " pdb=" H ILE B 496 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 TYR C 495 " pdb=" HD2 TYR C 495 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE2 TYR B 495 " pdb=" HE2 TYR B 495 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 29941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 44382 2.49 - 4.97: 7550 4.97 - 7.46: 1870 7.46 - 9.95: 126 9.95 - 12.43: 42 Bond angle restraints: 53970 Sorted by residual: angle pdb=" CA HIS D 532 " pdb=" CB HIS D 532 " pdb=" CG HIS D 532 " ideal model delta sigma weight residual 113.80 119.62 -5.82 1.00e+00 1.00e+00 3.38e+01 angle pdb=" CA HIS C 532 " pdb=" CB HIS C 532 " pdb=" CG HIS C 532 " ideal model delta sigma weight residual 113.80 119.61 -5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" CA HIS I 532 " pdb=" CB HIS I 532 " pdb=" CG HIS I 532 " ideal model delta sigma weight residual 113.80 119.60 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA HIS B 532 " pdb=" CB HIS B 532 " pdb=" CG HIS B 532 " ideal model delta sigma weight residual 113.80 119.60 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA HIS G 532 " pdb=" CB HIS G 532 " pdb=" CG HIS G 532 " ideal model delta sigma weight residual 113.80 119.59 -5.79 1.00e+00 1.00e+00 3.35e+01 ... (remaining 53965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.64: 12768 13.64 - 27.28: 910 27.28 - 40.92: 294 40.92 - 54.56: 84 54.56 - 68.20: 168 Dihedral angle restraints: 14224 sinusoidal: 7658 harmonic: 6566 Sorted by residual: dihedral pdb=" CA SER F 443 " pdb=" C SER F 443 " pdb=" N PHE F 444 " pdb=" CA PHE F 444 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER J 443 " pdb=" C SER J 443 " pdb=" N PHE J 444 " pdb=" CA PHE J 444 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER G 443 " pdb=" C SER G 443 " pdb=" N PHE G 444 " pdb=" CA PHE G 444 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 14221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1019 0.050 - 0.101: 745 0.101 - 0.151: 280 0.151 - 0.202: 154 0.202 - 0.252: 42 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA GLU K 413 " pdb=" N GLU K 413 " pdb=" C GLU K 413 " pdb=" CB GLU K 413 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA GLU D 413 " pdb=" N GLU D 413 " pdb=" C GLU D 413 " pdb=" CB GLU D 413 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA GLU C 413 " pdb=" N GLU C 413 " pdb=" C GLU C 413 " pdb=" CB GLU C 413 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2237 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 517 " -0.090 9.50e-02 1.11e+02 6.21e-02 6.73e+01 pdb=" NE ARG C 517 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 517 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG C 517 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 517 " 0.060 2.00e-02 2.50e+03 pdb="HH11 ARG C 517 " -0.030 2.00e-02 2.50e+03 pdb="HH12 ARG C 517 " -0.038 2.00e-02 2.50e+03 pdb="HH21 ARG C 517 " -0.119 2.00e-02 2.50e+03 pdb="HH22 ARG C 517 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 517 " -0.090 9.50e-02 1.11e+02 6.21e-02 6.73e+01 pdb=" NE ARG D 517 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D 517 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG D 517 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 517 " 0.059 2.00e-02 2.50e+03 pdb="HH11 ARG D 517 " -0.030 2.00e-02 2.50e+03 pdb="HH12 ARG D 517 " -0.039 2.00e-02 2.50e+03 pdb="HH21 ARG D 517 " -0.119 2.00e-02 2.50e+03 pdb="HH22 ARG D 517 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 517 " 0.090 9.50e-02 1.11e+02 6.21e-02 6.73e+01 pdb=" NE ARG I 517 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG I 517 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG I 517 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 517 " -0.059 2.00e-02 2.50e+03 pdb="HH11 ARG I 517 " 0.030 2.00e-02 2.50e+03 pdb="HH12 ARG I 517 " 0.039 2.00e-02 2.50e+03 pdb="HH21 ARG I 517 " 0.119 2.00e-02 2.50e+03 pdb="HH22 ARG I 517 " -0.059 2.00e-02 2.50e+03 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2449 2.24 - 2.83: 52849 2.83 - 3.42: 76785 3.42 - 4.01: 102724 4.01 - 4.60: 151308 Nonbonded interactions: 386115 Sorted by model distance: nonbonded pdb=" HH TYR N 495 " pdb=" OE1 GLU N 515 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR B 495 " pdb=" OE1 GLU B 515 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR M 495 " pdb=" OE1 GLU M 515 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR F 495 " pdb=" OE1 GLU F 515 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR A 495 " pdb=" OE1 GLU A 515 " model vdw 1.649 2.450 ... (remaining 386110 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.310 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 22.260 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 15484 Z= 0.846 Angle : 1.884 5.980 21042 Z= 1.289 Chirality : 0.084 0.252 2240 Planarity : 0.011 0.057 2814 Dihedral : 12.069 68.202 5684 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.19), residues: 1862 helix: -1.88 (0.16), residues: 476 sheet: 4.02 (0.19), residues: 574 loop : -1.21 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 517 TYR 0.064 0.017 TYR E 462 PHE 0.027 0.011 PHE E 444 TRP 0.022 0.010 TRP M 526 HIS 0.011 0.003 HIS L 520 Details of bonding type rmsd covalent geometry : bond 0.01346 (15484) covalent geometry : angle 1.88409 (21042) hydrogen bonds : bond 0.20133 ( 658) hydrogen bonds : angle 6.96922 ( 1806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 GLU cc_start: 0.8406 (pt0) cc_final: 0.8141 (pt0) REVERT: A 460 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8208 (ttm-80) REVERT: B 460 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8106 (ttm-80) REVERT: B 509 ARG cc_start: 0.8257 (mmt180) cc_final: 0.8048 (mmp80) REVERT: C 454 GLU cc_start: 0.8705 (tt0) cc_final: 0.8443 (tt0) REVERT: C 456 MET cc_start: 0.8601 (mmm) cc_final: 0.8236 (mpp) REVERT: C 460 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.7763 (ttp-110) REVERT: D 454 GLU cc_start: 0.8655 (tt0) cc_final: 0.8349 (tt0) REVERT: D 460 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8219 (ttm-80) REVERT: D 489 ASP cc_start: 0.8737 (m-30) cc_final: 0.8463 (p0) REVERT: D 509 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7970 (mmp80) REVERT: E 413 GLU cc_start: 0.8406 (pt0) cc_final: 0.8197 (pt0) REVERT: E 460 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8054 (ttt-90) REVERT: E 489 ASP cc_start: 0.8650 (m-30) cc_final: 0.8329 (p0) REVERT: F 460 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.7645 (ttp-110) REVERT: G 413 GLU cc_start: 0.8417 (pt0) cc_final: 0.8160 (pt0) REVERT: G 423 GLU cc_start: 0.7809 (tp30) cc_final: 0.7511 (pt0) REVERT: G 454 GLU cc_start: 0.8690 (tt0) cc_final: 0.8343 (tt0) REVERT: G 460 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.7379 (ttp-110) REVERT: G 489 ASP cc_start: 0.8716 (m-30) cc_final: 0.8493 (p0) REVERT: G 509 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7938 (mmp80) REVERT: H 413 GLU cc_start: 0.8470 (pt0) cc_final: 0.8200 (pt0) REVERT: H 460 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8164 (ttm-80) REVERT: I 460 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.8085 (ttm-80) REVERT: J 454 GLU cc_start: 0.8709 (tt0) cc_final: 0.8471 (tt0) REVERT: J 456 MET cc_start: 0.8642 (mmm) cc_final: 0.8265 (mpp) REVERT: J 460 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.7721 (ttp-110) REVERT: J 509 ARG cc_start: 0.8154 (mmt180) cc_final: 0.7939 (mmp80) REVERT: K 413 GLU cc_start: 0.8328 (pt0) cc_final: 0.8074 (pt0) REVERT: K 454 GLU cc_start: 0.8680 (tt0) cc_final: 0.8322 (tt0) REVERT: K 460 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8227 (ttm-80) REVERT: K 489 ASP cc_start: 0.8751 (m-30) cc_final: 0.8460 (p0) REVERT: K 509 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7890 (mmp80) REVERT: L 460 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8044 (ttt-90) REVERT: L 489 ASP cc_start: 0.8690 (m-30) cc_final: 0.8376 (p0) REVERT: L 509 ARG cc_start: 0.8206 (mmt180) cc_final: 0.7992 (mmp80) REVERT: M 460 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.7576 (ttp-110) REVERT: N 413 GLU cc_start: 0.8405 (pt0) cc_final: 0.8139 (pt0) REVERT: N 423 GLU cc_start: 0.7845 (tp30) cc_final: 0.7574 (pt0) REVERT: N 454 GLU cc_start: 0.8700 (tt0) cc_final: 0.8345 (tt0) REVERT: N 460 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7666 (ttp-110) REVERT: N 489 ASP cc_start: 0.8746 (m-30) cc_final: 0.8527 (p0) REVERT: N 509 ARG cc_start: 0.8232 (mmt180) cc_final: 0.8031 (mmp80) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 1.3626 time to fit residues: 633.6177 Evaluate side-chains 373 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN I 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.170177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141201 restraints weight = 41237.246| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.68 r_work: 0.3506 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15484 Z= 0.179 Angle : 0.692 5.510 21042 Z= 0.383 Chirality : 0.045 0.138 2240 Planarity : 0.006 0.053 2814 Dihedral : 5.809 24.728 2044 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.93 % Allowed : 7.39 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.20), residues: 1862 helix: -0.41 (0.21), residues: 476 sheet: 3.03 (0.22), residues: 616 loop : -0.90 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 410 TYR 0.009 0.002 TYR L 433 PHE 0.011 0.002 PHE L 444 TRP 0.009 0.002 TRP N 519 HIS 0.004 0.001 HIS E 520 Details of bonding type rmsd covalent geometry : bond 0.00367 (15484) covalent geometry : angle 0.69219 (21042) hydrogen bonds : bond 0.07146 ( 658) hydrogen bonds : angle 5.45202 ( 1806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 398 time to evaluate : 0.668 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: A 453 VAL cc_start: 0.8609 (t) cc_final: 0.8378 (m) REVERT: A 460 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7749 (ttm-80) REVERT: A 525 LYS cc_start: 0.7770 (tttp) cc_final: 0.7399 (ttpp) REVERT: B 509 ARG cc_start: 0.7874 (mmt180) cc_final: 0.7622 (mmp80) REVERT: C 454 GLU cc_start: 0.8602 (tt0) cc_final: 0.8364 (tt0) REVERT: C 456 MET cc_start: 0.8544 (mmm) cc_final: 0.8221 (mpp) REVERT: C 460 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7441 (ttp-110) REVERT: D 454 GLU cc_start: 0.8590 (tt0) cc_final: 0.8230 (tt0) REVERT: D 509 ARG cc_start: 0.7716 (mmt180) cc_final: 0.7478 (mmp80) REVERT: E 460 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: F 454 GLU cc_start: 0.8466 (tt0) cc_final: 0.8242 (tt0) REVERT: G 454 GLU cc_start: 0.8506 (tt0) cc_final: 0.8157 (tt0) REVERT: G 456 MET cc_start: 0.8571 (mmm) cc_final: 0.8302 (mmm) REVERT: G 460 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7472 (ttp-110) REVERT: H 453 VAL cc_start: 0.8611 (t) cc_final: 0.8381 (m) REVERT: H 460 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7732 (ttm-80) REVERT: H 525 LYS cc_start: 0.7779 (tttp) cc_final: 0.7418 (ttpp) REVERT: J 454 GLU cc_start: 0.8610 (tt0) cc_final: 0.8351 (tt0) REVERT: J 456 MET cc_start: 0.8571 (mmm) cc_final: 0.8258 (mpp) REVERT: J 460 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7444 (ttp-110) REVERT: K 454 GLU cc_start: 0.8594 (tt0) cc_final: 0.8237 (tt0) REVERT: K 460 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: K 509 ARG cc_start: 0.7698 (mmt180) cc_final: 0.7457 (mmp80) REVERT: M 454 GLU cc_start: 0.8497 (tt0) cc_final: 0.8265 (tt0) REVERT: M 460 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7377 (ttp-110) REVERT: N 454 GLU cc_start: 0.8525 (tt0) cc_final: 0.8182 (tt0) REVERT: N 456 MET cc_start: 0.8538 (mmm) cc_final: 0.8265 (mmm) REVERT: N 460 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7457 (ttp-110) outliers start: 15 outliers final: 2 residues processed: 400 average time/residue: 1.4361 time to fit residues: 620.9257 Evaluate side-chains 382 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain H residue 474 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 500 GLN B 465 ASN C 465 ASN D 465 ASN E 465 ASN F 465 ASN G 465 ASN H 465 ASN H 500 GLN I 465 ASN J 465 ASN K 465 ASN K 528 ASN L 465 ASN M 465 ASN M 528 ASN N 412 GLN N 465 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.167229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138112 restraints weight = 41292.409| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.64 r_work: 0.3470 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15484 Z= 0.198 Angle : 0.673 7.391 21042 Z= 0.371 Chirality : 0.048 0.156 2240 Planarity : 0.006 0.070 2814 Dihedral : 5.488 24.986 2044 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.61 % Allowed : 7.89 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.20), residues: 1862 helix: -0.33 (0.22), residues: 476 sheet: 3.14 (0.22), residues: 616 loop : -1.28 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 521 TYR 0.009 0.002 TYR G 495 PHE 0.015 0.002 PHE L 444 TRP 0.011 0.002 TRP N 519 HIS 0.005 0.002 HIS C 532 Details of bonding type rmsd covalent geometry : bond 0.00423 (15484) covalent geometry : angle 0.67328 (21042) hydrogen bonds : bond 0.06592 ( 658) hydrogen bonds : angle 4.95344 ( 1806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 390 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7751 (ttm-80) REVERT: A 509 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7627 (mmm160) REVERT: A 525 LYS cc_start: 0.7762 (tttp) cc_final: 0.7385 (ttpp) REVERT: C 454 GLU cc_start: 0.8662 (tt0) cc_final: 0.8435 (tt0) REVERT: C 456 MET cc_start: 0.8515 (mmm) cc_final: 0.8284 (mpp) REVERT: C 460 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7724 (ttm-80) REVERT: C 509 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7486 (mmp80) REVERT: D 454 GLU cc_start: 0.8643 (tt0) cc_final: 0.8370 (tt0) REVERT: E 460 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7721 (ttt-90) REVERT: F 460 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7714 (ttm-80) REVERT: F 509 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7739 (mmp80) REVERT: G 423 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: G 454 GLU cc_start: 0.8505 (tt0) cc_final: 0.8160 (tt0) REVERT: G 460 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7664 (ttm-80) REVERT: H 460 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7756 (ttm-80) REVERT: H 509 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7608 (mmm160) REVERT: H 525 LYS cc_start: 0.7759 (tttp) cc_final: 0.7392 (ttpp) REVERT: J 454 GLU cc_start: 0.8663 (tt0) cc_final: 0.8409 (tt0) REVERT: J 456 MET cc_start: 0.8541 (mmm) cc_final: 0.8311 (mpp) REVERT: J 460 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7720 (ttm-80) REVERT: J 509 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7492 (mmp80) REVERT: K 454 GLU cc_start: 0.8668 (tt0) cc_final: 0.8393 (tt0) REVERT: K 460 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7727 (ttm-80) REVERT: M 460 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7670 (ttm-80) REVERT: M 509 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7727 (mmp80) REVERT: N 423 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: N 454 GLU cc_start: 0.8493 (tt0) cc_final: 0.8150 (tt0) REVERT: N 460 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7669 (ttm-80) outliers start: 26 outliers final: 12 residues processed: 390 average time/residue: 1.4285 time to fit residues: 602.0463 Evaluate side-chains 389 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 369 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain F residue 509 ARG Chi-restraints excluded: chain G residue 423 GLU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 509 ARG Chi-restraints excluded: chain N residue 423 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 GLN F 412 GLN K 412 GLN M 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.167917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139032 restraints weight = 41153.908| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.63 r_work: 0.3495 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15484 Z= 0.161 Angle : 0.605 6.290 21042 Z= 0.333 Chirality : 0.046 0.151 2240 Planarity : 0.007 0.077 2814 Dihedral : 5.383 27.253 2044 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.61 % Allowed : 8.76 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1862 helix: -0.11 (0.22), residues: 476 sheet: 2.60 (0.22), residues: 686 loop : -0.75 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 509 TYR 0.007 0.002 TYR K 462 PHE 0.010 0.002 PHE D 444 TRP 0.009 0.002 TRP K 519 HIS 0.003 0.001 HIS N 459 Details of bonding type rmsd covalent geometry : bond 0.00341 (15484) covalent geometry : angle 0.60485 (21042) hydrogen bonds : bond 0.05834 ( 658) hydrogen bonds : angle 4.80123 ( 1806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 383 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7708 (ttm-80) REVERT: A 509 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7567 (mmm160) REVERT: A 525 LYS cc_start: 0.7679 (tttp) cc_final: 0.7330 (ttpp) REVERT: C 454 GLU cc_start: 0.8607 (tt0) cc_final: 0.8356 (tt0) REVERT: C 456 MET cc_start: 0.8478 (mmm) cc_final: 0.8222 (mpp) REVERT: C 460 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7690 (ttm-80) REVERT: C 509 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7430 (mmt90) REVERT: D 454 GLU cc_start: 0.8628 (tt0) cc_final: 0.8290 (tt0) REVERT: E 460 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7746 (ttt-90) REVERT: F 429 ASP cc_start: 0.8648 (t0) cc_final: 0.8438 (t70) REVERT: F 460 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7727 (ttm-80) REVERT: F 509 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7703 (mmp80) REVERT: G 423 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: G 454 GLU cc_start: 0.8508 (tt0) cc_final: 0.8225 (tt0) REVERT: G 460 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: H 460 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: H 509 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7549 (mmm160) REVERT: H 525 LYS cc_start: 0.7674 (tttp) cc_final: 0.7326 (ttpp) REVERT: J 454 GLU cc_start: 0.8653 (tt0) cc_final: 0.8390 (tt0) REVERT: J 456 MET cc_start: 0.8504 (mmm) cc_final: 0.8250 (mpp) REVERT: J 460 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7682 (ttm-80) REVERT: J 509 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7429 (mmp80) REVERT: K 454 GLU cc_start: 0.8634 (tt0) cc_final: 0.8340 (tt0) REVERT: K 460 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7720 (ttm-80) REVERT: L 509 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7644 (mmm160) REVERT: M 460 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7677 (ttm-80) REVERT: N 423 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: N 454 GLU cc_start: 0.8495 (tt0) cc_final: 0.8172 (tt0) REVERT: N 460 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7653 (ttm-80) outliers start: 26 outliers final: 10 residues processed: 383 average time/residue: 1.3966 time to fit residues: 578.3659 Evaluate side-chains 396 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 379 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 423 GLU Chi-restraints excluded: chain F residue 509 ARG Chi-restraints excluded: chain G residue 423 GLU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain N residue 423 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 3.9990 chunk 137 optimal weight: 0.0070 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN I 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.145341 restraints weight = 41663.386| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.59 r_work: 0.3507 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15484 Z= 0.139 Angle : 0.563 5.592 21042 Z= 0.308 Chirality : 0.045 0.152 2240 Planarity : 0.007 0.077 2814 Dihedral : 5.232 27.845 2044 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.18 % Allowed : 10.00 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.20), residues: 1862 helix: 0.10 (0.22), residues: 476 sheet: 2.60 (0.22), residues: 686 loop : -0.60 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 507 TYR 0.006 0.001 TYR N 462 PHE 0.010 0.001 PHE M 444 TRP 0.008 0.001 TRP K 519 HIS 0.003 0.001 HIS I 484 Details of bonding type rmsd covalent geometry : bond 0.00290 (15484) covalent geometry : angle 0.56325 (21042) hydrogen bonds : bond 0.05190 ( 658) hydrogen bonds : angle 4.56986 ( 1806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 398 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7745 (ttm-80) REVERT: A 509 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7581 (mmm160) REVERT: A 525 LYS cc_start: 0.7629 (tttp) cc_final: 0.7254 (ttpp) REVERT: C 454 GLU cc_start: 0.8555 (tt0) cc_final: 0.8322 (tt0) REVERT: C 456 MET cc_start: 0.8434 (mmm) cc_final: 0.8208 (mpp) REVERT: C 460 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: C 509 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7460 (mmt90) REVERT: D 454 GLU cc_start: 0.8616 (tt0) cc_final: 0.8288 (tt0) REVERT: E 423 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: E 460 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7796 (ttt-90) REVERT: F 460 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: G 423 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: G 454 GLU cc_start: 0.8513 (tt0) cc_final: 0.8181 (tt0) REVERT: G 460 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: H 460 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7730 (ttm-80) REVERT: H 509 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7590 (mmm160) REVERT: H 525 LYS cc_start: 0.7606 (tttp) cc_final: 0.7239 (ttpp) REVERT: I 423 GLU cc_start: 0.8008 (pt0) cc_final: 0.7639 (pt0) REVERT: J 454 GLU cc_start: 0.8593 (tt0) cc_final: 0.8355 (tt0) REVERT: J 456 MET cc_start: 0.8435 (mmm) cc_final: 0.8211 (mpp) REVERT: J 460 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7687 (ttm-80) REVERT: J 509 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7401 (mmp80) REVERT: K 454 GLU cc_start: 0.8619 (tt0) cc_final: 0.8323 (tt0) REVERT: K 460 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7739 (ttm-80) REVERT: M 460 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7742 (ttm-80) REVERT: N 423 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: N 454 GLU cc_start: 0.8452 (tt0) cc_final: 0.8129 (tt0) outliers start: 19 outliers final: 6 residues processed: 398 average time/residue: 1.4802 time to fit residues: 637.4473 Evaluate side-chains 405 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 392 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain G residue 423 GLU Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain N residue 423 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 119 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 176 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN B 412 GLN H 412 GLN L 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143234 restraints weight = 41384.720| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.64 r_work: 0.3478 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15484 Z= 0.163 Angle : 0.593 6.306 21042 Z= 0.325 Chirality : 0.045 0.150 2240 Planarity : 0.007 0.080 2814 Dihedral : 5.275 28.726 2044 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.37 % Allowed : 10.12 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.21), residues: 1862 helix: 0.08 (0.22), residues: 476 sheet: 2.61 (0.23), residues: 686 loop : -0.62 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 507 TYR 0.008 0.002 TYR G 462 PHE 0.011 0.002 PHE D 444 TRP 0.008 0.002 TRP K 519 HIS 0.003 0.001 HIS I 484 Details of bonding type rmsd covalent geometry : bond 0.00349 (15484) covalent geometry : angle 0.59307 (21042) hydrogen bonds : bond 0.05655 ( 658) hydrogen bonds : angle 4.61592 ( 1806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 390 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: A 509 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7608 (mmm160) REVERT: A 525 LYS cc_start: 0.7652 (tttp) cc_final: 0.7285 (ttpp) REVERT: C 454 GLU cc_start: 0.8614 (tt0) cc_final: 0.8391 (tt0) REVERT: C 460 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7715 (ttm-80) REVERT: C 509 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7494 (mmt90) REVERT: D 454 GLU cc_start: 0.8655 (tt0) cc_final: 0.8334 (tt0) REVERT: D 521 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7721 (ttp80) REVERT: E 423 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: E 460 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7802 (ttm-80) REVERT: E 474 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8717 (mp) REVERT: F 460 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7759 (ttm-80) REVERT: G 454 GLU cc_start: 0.8588 (tt0) cc_final: 0.8237 (tt0) REVERT: G 460 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7661 (ttm-80) REVERT: H 460 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7739 (ttm-80) REVERT: H 509 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7608 (mmm160) REVERT: H 525 LYS cc_start: 0.7646 (tttp) cc_final: 0.7283 (ttpp) REVERT: I 423 GLU cc_start: 0.7946 (pt0) cc_final: 0.7704 (pt0) REVERT: I 509 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7664 (mmm160) REVERT: J 454 GLU cc_start: 0.8632 (tt0) cc_final: 0.8406 (tt0) REVERT: J 460 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7676 (ttm-80) REVERT: K 454 GLU cc_start: 0.8665 (tt0) cc_final: 0.8338 (tt0) REVERT: L 454 GLU cc_start: 0.8428 (tt0) cc_final: 0.8224 (tt0) REVERT: L 474 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8713 (mp) REVERT: M 460 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7728 (ttm-80) REVERT: N 423 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: N 454 GLU cc_start: 0.8468 (tt0) cc_final: 0.8144 (tt0) outliers start: 22 outliers final: 7 residues processed: 390 average time/residue: 1.4529 time to fit residues: 611.6135 Evaluate side-chains 397 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 381 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain N residue 423 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN L 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.172906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142997 restraints weight = 41375.507| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.78 r_work: 0.3575 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15484 Z= 0.145 Angle : 0.571 5.928 21042 Z= 0.313 Chirality : 0.045 0.148 2240 Planarity : 0.007 0.081 2814 Dihedral : 5.235 29.034 2044 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.49 % Allowed : 10.87 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.21), residues: 1862 helix: 0.18 (0.22), residues: 476 sheet: 2.61 (0.22), residues: 686 loop : -0.55 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 507 TYR 0.007 0.001 TYR G 462 PHE 0.010 0.001 PHE I 430 TRP 0.008 0.001 TRP D 519 HIS 0.003 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00305 (15484) covalent geometry : angle 0.57124 (21042) hydrogen bonds : bond 0.05321 ( 658) hydrogen bonds : angle 4.54650 ( 1806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 389 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7693 (ttm-80) REVERT: A 509 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7567 (mmm160) REVERT: A 525 LYS cc_start: 0.7637 (tttp) cc_final: 0.7272 (ttpp) REVERT: C 454 GLU cc_start: 0.8536 (tt0) cc_final: 0.8292 (tt0) REVERT: C 460 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7651 (ttm-80) REVERT: C 509 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7488 (mmt90) REVERT: D 454 GLU cc_start: 0.8603 (tt0) cc_final: 0.8276 (tt0) REVERT: D 521 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7674 (ttp80) REVERT: E 423 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7333 (pt0) REVERT: E 460 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7740 (ttm-80) REVERT: E 474 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8723 (mp) REVERT: F 423 GLU cc_start: 0.7927 (pt0) cc_final: 0.7523 (pt0) REVERT: F 460 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: F 521 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7492 (ttp80) REVERT: G 454 GLU cc_start: 0.8541 (tt0) cc_final: 0.8189 (tt0) REVERT: G 460 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7605 (ttm-80) REVERT: H 460 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7705 (ttm-80) REVERT: H 509 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7568 (mmm160) REVERT: H 525 LYS cc_start: 0.7628 (tttp) cc_final: 0.7270 (ttpp) REVERT: I 423 GLU cc_start: 0.7887 (pt0) cc_final: 0.7633 (pt0) REVERT: I 509 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7640 (mmm160) REVERT: J 454 GLU cc_start: 0.8567 (tt0) cc_final: 0.8327 (tt0) REVERT: J 460 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7620 (ttm-80) REVERT: J 509 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7399 (mmp80) REVERT: K 454 GLU cc_start: 0.8606 (tt0) cc_final: 0.8321 (tt0) REVERT: K 460 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7680 (ttm-80) REVERT: K 521 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7547 (ttp80) REVERT: L 413 GLU cc_start: 0.7907 (pt0) cc_final: 0.7636 (pt0) REVERT: L 423 GLU cc_start: 0.7896 (pt0) cc_final: 0.7586 (pt0) REVERT: L 454 GLU cc_start: 0.8367 (tt0) cc_final: 0.8164 (tt0) REVERT: L 474 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8714 (mp) REVERT: M 423 GLU cc_start: 0.7974 (pt0) cc_final: 0.7578 (pt0) REVERT: M 460 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7682 (ttm-80) REVERT: M 521 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7508 (ttp80) REVERT: N 423 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: N 454 GLU cc_start: 0.8408 (tt0) cc_final: 0.8088 (tt0) outliers start: 24 outliers final: 7 residues processed: 391 average time/residue: 1.4668 time to fit residues: 619.4645 Evaluate side-chains 409 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 389 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 521 ARG Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain M residue 521 ARG Chi-restraints excluded: chain N residue 423 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 120 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 119 optimal weight: 0.0270 chunk 37 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN L 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.173236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143224 restraints weight = 41401.585| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.77 r_work: 0.3573 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15484 Z= 0.141 Angle : 0.563 5.782 21042 Z= 0.308 Chirality : 0.045 0.147 2240 Planarity : 0.007 0.078 2814 Dihedral : 5.195 29.058 2044 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.24 % Allowed : 11.37 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.21), residues: 1862 helix: 0.28 (0.22), residues: 476 sheet: 2.61 (0.23), residues: 686 loop : -0.51 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 507 TYR 0.006 0.001 TYR G 462 PHE 0.010 0.001 PHE D 444 TRP 0.008 0.001 TRP K 519 HIS 0.003 0.001 HIS I 484 Details of bonding type rmsd covalent geometry : bond 0.00297 (15484) covalent geometry : angle 0.56340 (21042) hydrogen bonds : bond 0.05187 ( 658) hydrogen bonds : angle 4.49749 ( 1806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 391 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7687 (ttm-80) REVERT: A 509 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7572 (mmm160) REVERT: A 525 LYS cc_start: 0.7625 (tttp) cc_final: 0.7266 (ttpp) REVERT: C 454 GLU cc_start: 0.8532 (tt0) cc_final: 0.8289 (tt0) REVERT: C 460 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7649 (ttm-80) REVERT: C 509 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7435 (mmt90) REVERT: D 423 GLU cc_start: 0.7864 (pt0) cc_final: 0.7470 (pt0) REVERT: D 454 GLU cc_start: 0.8609 (tt0) cc_final: 0.8285 (tt0) REVERT: D 521 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7677 (ttp80) REVERT: E 423 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: E 460 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7748 (ttt-90) REVERT: E 474 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8714 (mp) REVERT: F 423 GLU cc_start: 0.7927 (pt0) cc_final: 0.7508 (pt0) REVERT: F 460 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7716 (ttm-80) REVERT: F 521 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7488 (ttp80) REVERT: G 423 GLU cc_start: 0.7926 (pt0) cc_final: 0.7568 (pt0) REVERT: G 454 GLU cc_start: 0.8538 (tt0) cc_final: 0.8189 (tt0) REVERT: G 460 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7612 (ttm-80) REVERT: H 460 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7695 (ttm-80) REVERT: H 509 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7564 (mmm160) REVERT: H 525 LYS cc_start: 0.7629 (tttp) cc_final: 0.7275 (ttpp) REVERT: I 423 GLU cc_start: 0.7919 (pt0) cc_final: 0.7658 (pt0) REVERT: I 509 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7635 (mmm160) REVERT: J 454 GLU cc_start: 0.8562 (tt0) cc_final: 0.8321 (tt0) REVERT: J 460 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7612 (ttm-80) REVERT: J 509 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7387 (mmp80) REVERT: K 423 GLU cc_start: 0.7876 (pt0) cc_final: 0.7474 (pt0) REVERT: K 454 GLU cc_start: 0.8608 (tt0) cc_final: 0.8323 (tt0) REVERT: K 460 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7682 (ttm-80) REVERT: K 521 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7681 (ttp80) REVERT: L 413 GLU cc_start: 0.7904 (pt0) cc_final: 0.7622 (pt0) REVERT: L 423 GLU cc_start: 0.7880 (pt0) cc_final: 0.7553 (pt0) REVERT: L 454 GLU cc_start: 0.8351 (tt0) cc_final: 0.8145 (tt0) REVERT: L 474 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (mp) REVERT: M 423 GLU cc_start: 0.7987 (pt0) cc_final: 0.7577 (pt0) REVERT: M 460 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7687 (ttm-80) REVERT: M 521 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7511 (ttp80) REVERT: N 423 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: N 454 GLU cc_start: 0.8416 (tt0) cc_final: 0.8093 (tt0) outliers start: 20 outliers final: 6 residues processed: 394 average time/residue: 1.4805 time to fit residues: 629.9582 Evaluate side-chains 406 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 387 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 521 ARG Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain M residue 521 ARG Chi-restraints excluded: chain N residue 423 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 150 optimal weight: 0.0670 chunk 98 optimal weight: 0.0010 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.7326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN L 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.174385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144598 restraints weight = 41437.347| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.76 r_work: 0.3594 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15484 Z= 0.118 Angle : 0.533 5.072 21042 Z= 0.290 Chirality : 0.044 0.144 2240 Planarity : 0.007 0.082 2814 Dihedral : 5.106 28.909 2044 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.12 % Allowed : 12.17 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.21), residues: 1862 helix: 0.46 (0.23), residues: 476 sheet: 2.58 (0.23), residues: 686 loop : -0.41 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 507 TYR 0.005 0.001 TYR G 462 PHE 0.012 0.001 PHE I 430 TRP 0.007 0.001 TRP K 519 HIS 0.002 0.001 HIS K 520 Details of bonding type rmsd covalent geometry : bond 0.00242 (15484) covalent geometry : angle 0.53302 (21042) hydrogen bonds : bond 0.04643 ( 658) hydrogen bonds : angle 4.36069 ( 1806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 396 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: A 509 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7550 (mmm160) REVERT: A 525 LYS cc_start: 0.7591 (tttp) cc_final: 0.7239 (ttpp) REVERT: B 485 VAL cc_start: 0.8259 (t) cc_final: 0.7999 (t) REVERT: C 454 GLU cc_start: 0.8496 (tt0) cc_final: 0.8253 (tt0) REVERT: C 460 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7765 (ttm-80) REVERT: C 509 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7424 (mmt90) REVERT: D 423 GLU cc_start: 0.7837 (pt0) cc_final: 0.7442 (pt0) REVERT: D 454 GLU cc_start: 0.8590 (tt0) cc_final: 0.8305 (tt0) REVERT: D 521 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7686 (ttp80) REVERT: E 423 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: E 460 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7750 (ttm-80) REVERT: E 474 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8668 (mp) REVERT: F 423 GLU cc_start: 0.7954 (pt0) cc_final: 0.7565 (pt0) REVERT: F 460 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7745 (ttm-80) REVERT: F 521 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7471 (ttp80) REVERT: G 423 GLU cc_start: 0.7937 (pt0) cc_final: 0.7580 (pt0) REVERT: G 454 GLU cc_start: 0.8494 (tt0) cc_final: 0.8144 (tt0) REVERT: G 460 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7616 (ttm-80) REVERT: H 460 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: H 509 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7557 (mmm160) REVERT: H 525 LYS cc_start: 0.7593 (tttp) cc_final: 0.7242 (ttpp) REVERT: I 423 GLU cc_start: 0.7897 (pt0) cc_final: 0.7625 (pt0) REVERT: I 485 VAL cc_start: 0.8283 (t) cc_final: 0.8000 (t) REVERT: J 454 GLU cc_start: 0.8502 (tt0) cc_final: 0.8260 (tt0) REVERT: J 460 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: J 509 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7364 (mmp80) REVERT: K 423 GLU cc_start: 0.7849 (pt0) cc_final: 0.7436 (pt0) REVERT: K 454 GLU cc_start: 0.8575 (tt0) cc_final: 0.8285 (tt0) REVERT: K 460 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7669 (ttm-80) REVERT: K 521 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7670 (ttp80) REVERT: L 413 GLU cc_start: 0.7845 (pt0) cc_final: 0.7552 (pt0) REVERT: L 423 GLU cc_start: 0.7883 (pt0) cc_final: 0.7542 (pt0) REVERT: L 454 GLU cc_start: 0.8353 (tt0) cc_final: 0.8116 (tt0) REVERT: L 474 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8669 (mp) REVERT: M 423 GLU cc_start: 0.7991 (pt0) cc_final: 0.7602 (pt0) REVERT: M 460 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7715 (ttm-80) REVERT: M 521 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7482 (ttp80) REVERT: N 454 GLU cc_start: 0.8402 (tt0) cc_final: 0.8071 (tt0) outliers start: 18 outliers final: 6 residues processed: 398 average time/residue: 1.5863 time to fit residues: 681.7196 Evaluate side-chains 409 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 392 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 521 ARG Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain M residue 521 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.174325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144637 restraints weight = 41283.165| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.75 r_work: 0.3594 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15484 Z= 0.125 Angle : 0.539 5.165 21042 Z= 0.293 Chirality : 0.044 0.144 2240 Planarity : 0.007 0.078 2814 Dihedral : 5.065 28.615 2044 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.93 % Allowed : 12.30 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.21), residues: 1862 helix: 0.51 (0.23), residues: 476 sheet: 2.60 (0.23), residues: 686 loop : -0.38 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 507 TYR 0.005 0.001 TYR G 462 PHE 0.012 0.001 PHE I 430 TRP 0.007 0.001 TRP K 519 HIS 0.003 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00260 (15484) covalent geometry : angle 0.53920 (21042) hydrogen bonds : bond 0.04722 ( 658) hydrogen bonds : angle 4.33497 ( 1806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 392 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: A 509 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7549 (mmm160) REVERT: A 525 LYS cc_start: 0.7577 (tttp) cc_final: 0.7230 (ttpp) REVERT: B 485 VAL cc_start: 0.8264 (t) cc_final: 0.7988 (t) REVERT: C 454 GLU cc_start: 0.8512 (tt0) cc_final: 0.8283 (tt0) REVERT: C 460 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7751 (ttm-80) REVERT: C 509 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7430 (mmt90) REVERT: D 423 GLU cc_start: 0.7831 (pt0) cc_final: 0.7432 (pt0) REVERT: D 454 GLU cc_start: 0.8569 (tt0) cc_final: 0.8282 (tt0) REVERT: D 521 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7680 (ttp80) REVERT: E 423 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: E 460 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: E 474 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8667 (mp) REVERT: F 423 GLU cc_start: 0.7916 (pt0) cc_final: 0.7534 (pt0) REVERT: F 460 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7739 (ttm-80) REVERT: F 521 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7477 (ttp80) REVERT: G 423 GLU cc_start: 0.7919 (pt0) cc_final: 0.7587 (pt0) REVERT: G 454 GLU cc_start: 0.8505 (tt0) cc_final: 0.8136 (tt0) REVERT: G 460 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7674 (ttm-80) REVERT: H 460 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: H 509 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7558 (mmm160) REVERT: H 525 LYS cc_start: 0.7581 (tttp) cc_final: 0.7231 (ttpp) REVERT: I 423 GLU cc_start: 0.7903 (pt0) cc_final: 0.7624 (pt0) REVERT: I 485 VAL cc_start: 0.8268 (t) cc_final: 0.7984 (t) REVERT: J 454 GLU cc_start: 0.8502 (tt0) cc_final: 0.8277 (tt0) REVERT: J 460 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7401 (ttp-110) REVERT: J 509 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7336 (mmp80) REVERT: K 423 GLU cc_start: 0.7856 (pt0) cc_final: 0.7446 (pt0) REVERT: K 454 GLU cc_start: 0.8567 (tt0) cc_final: 0.8277 (tt0) REVERT: K 460 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7646 (ttm-80) REVERT: K 521 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7664 (ttp80) REVERT: L 413 GLU cc_start: 0.7888 (pt0) cc_final: 0.7581 (pt0) REVERT: L 423 GLU cc_start: 0.7868 (pt0) cc_final: 0.7522 (pt0) REVERT: L 454 GLU cc_start: 0.8354 (tt0) cc_final: 0.8116 (tt0) REVERT: L 474 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8670 (mp) REVERT: M 423 GLU cc_start: 0.7963 (pt0) cc_final: 0.7588 (pt0) REVERT: M 460 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: M 521 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7479 (ttp80) REVERT: N 454 GLU cc_start: 0.8399 (tt0) cc_final: 0.8073 (tt0) outliers start: 15 outliers final: 3 residues processed: 394 average time/residue: 1.4601 time to fit residues: 621.8423 Evaluate side-chains 406 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 392 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain F residue 521 ARG Chi-restraints excluded: chain H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain M residue 521 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 73 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.173722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144839 restraints weight = 41492.473| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.65 r_work: 0.3567 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15484 Z= 0.137 Angle : 0.553 5.583 21042 Z= 0.301 Chirality : 0.044 0.148 2240 Planarity : 0.007 0.078 2814 Dihedral : 5.069 28.504 2044 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.87 % Allowed : 12.61 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.21), residues: 1862 helix: 0.49 (0.23), residues: 476 sheet: 2.61 (0.23), residues: 686 loop : -0.40 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 507 TYR 0.006 0.001 TYR G 462 PHE 0.010 0.001 PHE D 444 TRP 0.007 0.001 TRP K 519 HIS 0.003 0.001 HIS I 484 Details of bonding type rmsd covalent geometry : bond 0.00289 (15484) covalent geometry : angle 0.55260 (21042) hydrogen bonds : bond 0.04932 ( 658) hydrogen bonds : angle 4.37330 ( 1806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12111.79 seconds wall clock time: 204 minutes 56.36 seconds (12296.36 seconds total)