Starting phenix.real_space_refine on Tue May 27 08:28:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t17_40956/05_2025/8t17_40956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t17_40956/05_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_40956/05_2025/8t17_40956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t17_40956/05_2025/8t17_40956.map" model { file = "/net/cci-nas-00/data/ceres_data/8t17_40956/05_2025/8t17_40956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t17_40956/05_2025/8t17_40956.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, N Time building chain proxies: 7.70, per 1000 atoms: 0.26 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: 6.91 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 3.33 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: 11.62 Time building geometry restraints manager: 8.48 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.510 Extract box with map and model: 1.200 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 56.050 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.022 0.010 TRP M 526 HIS 0.011 0.003 HIS L 520 PHE 0.027 0.011 PHE E 444 TYR 0.064 0.017 TYR E 462 ARG 0.005 0.001 ARG L 517 Details of bonding type rmsd hydrogen bonds : bond 0.20133 ( 658) hydrogen bonds : angle 6.96922 ( 1806) covalent geometry : bond 0.01346 (15484) covalent geometry : angle 1.88409 (21042) *********************** 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 : 2.438 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: 3.1208 time to fit residues: 1453.1983 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 : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.170028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139325 restraints weight = 40927.974| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.79 r_work: 0.3501 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15484 Z= 0.177 Angle : 0.686 5.581 21042 Z= 0.380 Chirality : 0.045 0.140 2240 Planarity : 0.006 0.052 2814 Dihedral : 5.809 24.705 2044 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.93 % Allowed : 7.27 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1862 helix: -0.44 (0.21), residues: 476 sheet: 3.04 (0.22), residues: 616 loop : -0.89 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 519 HIS 0.003 0.001 HIS A 532 PHE 0.011 0.002 PHE I 444 TYR 0.009 0.002 TYR L 433 ARG 0.004 0.001 ARG J 410 Details of bonding type rmsd hydrogen bonds : bond 0.07058 ( 658) hydrogen bonds : angle 5.42956 ( 1806) covalent geometry : bond 0.00353 (15484) covalent geometry : angle 0.68562 (21042) *********************** 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 414 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 399 time to evaluate : 2.593 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: 0.8617 (t) cc_final: 0.8388 (m) REVERT: A 460 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7757 (ttm-80) REVERT: A 525 LYS cc_start: 0.7781 (tttp) cc_final: 0.7417 (ttpp) REVERT: B 509 ARG cc_start: 0.7877 (mmt180) cc_final: 0.7625 (mmp80) REVERT: C 454 GLU cc_start: 0.8576 (tt0) cc_final: 0.8328 (tt0) REVERT: C 456 MET cc_start: 0.8539 (mmm) cc_final: 0.8214 (mpp) REVERT: C 460 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7459 (ttp-110) REVERT: D 454 GLU cc_start: 0.8590 (tt0) cc_final: 0.8232 (tt0) REVERT: D 509 ARG cc_start: 0.7709 (mmt180) cc_final: 0.7474 (mmp80) REVERT: E 460 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7716 (ttm-80) REVERT: G 454 GLU cc_start: 0.8506 (tt0) cc_final: 0.8161 (tt0) REVERT: G 456 MET cc_start: 0.8571 (mmm) cc_final: 0.8301 (mmm) REVERT: G 460 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7481 (ttp-110) REVERT: H 453 VAL cc_start: 0.8617 (t) cc_final: 0.8393 (m) REVERT: H 460 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: H 525 LYS cc_start: 0.7790 (tttp) cc_final: 0.7431 (ttpp) REVERT: I 460 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7792 (ttm-80) REVERT: J 454 GLU cc_start: 0.8606 (tt0) cc_final: 0.8345 (tt0) REVERT: J 456 MET cc_start: 0.8571 (mmm) cc_final: 0.8256 (mpp) REVERT: J 460 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7451 (ttp-110) REVERT: K 454 GLU cc_start: 0.8587 (tt0) cc_final: 0.8229 (tt0) REVERT: K 460 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: K 509 ARG cc_start: 0.7705 (mmt180) cc_final: 0.7459 (mmp80) REVERT: M 460 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7381 (ttp-110) REVERT: N 454 GLU cc_start: 0.8528 (tt0) cc_final: 0.8185 (tt0) REVERT: N 456 MET cc_start: 0.8532 (mmm) cc_final: 0.8261 (mmm) REVERT: N 460 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7463 (ttp-110) outliers start: 15 outliers final: 2 residues processed: 401 average time/residue: 3.3459 time to fit residues: 1451.3095 Evaluate side-chains 384 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 106 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN B 465 ASN G 465 ASN H 465 ASN H 500 GLN I 465 ASN J 465 ASN N 412 GLN N 465 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.166612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.136457 restraints weight = 41253.156| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.77 r_work: 0.3472 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15484 Z= 0.213 Angle : 0.689 7.364 21042 Z= 0.382 Chirality : 0.048 0.154 2240 Planarity : 0.006 0.068 2814 Dihedral : 5.580 25.639 2044 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.61 % Allowed : 7.52 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1862 helix: -0.38 (0.22), residues: 476 sheet: 3.10 (0.22), residues: 616 loop : -1.27 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 519 HIS 0.005 0.001 HIS C 532 PHE 0.014 0.002 PHE L 444 TYR 0.008 0.003 TYR G 495 ARG 0.005 0.001 ARG C 507 Details of bonding type rmsd hydrogen bonds : bond 0.07058 ( 658) hydrogen bonds : angle 5.09715 ( 1806) covalent geometry : bond 0.00454 (15484) covalent geometry : angle 0.68864 (21042) *********************** 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 405 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 379 time to evaluate : 2.338 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: A 460 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: A 509 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7201 (mmp80) REVERT: A 525 LYS cc_start: 0.7804 (tttp) cc_final: 0.7430 (ttpp) REVERT: C 454 GLU cc_start: 0.8648 (tt0) cc_final: 0.8427 (tt0) REVERT: C 456 MET cc_start: 0.8539 (mmm) cc_final: 0.8262 (mpp) REVERT: C 460 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7600 (ttp-110) REVERT: C 509 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7609 (mmp80) REVERT: D 454 GLU cc_start: 0.8628 (tt0) cc_final: 0.8303 (tt0) REVERT: E 460 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7734 (ttt-90) REVERT: E 509 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6929 (mmp80) REVERT: F 509 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7703 (mmp80) REVERT: G 423 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: G 454 GLU cc_start: 0.8488 (tt0) cc_final: 0.8154 (tt0) REVERT: H 460 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: H 509 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7200 (mmp80) REVERT: H 525 LYS cc_start: 0.7801 (tttp) cc_final: 0.7436 (ttpp) REVERT: I 460 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7777 (ttm-80) REVERT: J 454 GLU cc_start: 0.8659 (tt0) cc_final: 0.8415 (tt0) REVERT: J 456 MET cc_start: 0.8546 (mmm) cc_final: 0.8272 (mpp) REVERT: J 460 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7581 (ttp-110) REVERT: J 509 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7429 (mmp-170) REVERT: K 454 GLU cc_start: 0.8660 (tt0) cc_final: 0.8335 (tt0) REVERT: K 460 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7791 (ttm-80) REVERT: M 509 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7760 (mmp80) REVERT: N 423 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: N 454 GLU cc_start: 0.8505 (tt0) cc_final: 0.8166 (tt0) outliers start: 26 outliers final: 8 residues processed: 379 average time/residue: 3.3273 time to fit residues: 1361.1997 Evaluate side-chains 388 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 371 time to evaluate : 2.289 ------------------------------------------------------------------------------- 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 I residue 509 ARG Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain J residue 509 ARG 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 147 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 179 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 ASN D 412 GLN D 465 ASN E 465 ASN F 412 GLN F 465 ASN K 412 GLN K 465 ASN L 465 ASN M 412 GLN M 465 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141587 restraints weight = 41421.428| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.63 r_work: 0.3510 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3471 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= 0.124 Angle : 0.550 4.961 21042 Z= 0.300 Chirality : 0.044 0.148 2240 Planarity : 0.006 0.075 2814 Dihedral : 5.283 26.876 2044 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.43 % Allowed : 8.26 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1862 helix: 0.14 (0.22), residues: 476 sheet: 2.56 (0.22), residues: 686 loop : -0.58 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 519 HIS 0.003 0.001 HIS C 532 PHE 0.009 0.001 PHE E 444 TYR 0.004 0.001 TYR K 462 ARG 0.003 0.000 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 658) hydrogen bonds : angle 4.59556 ( 1806) covalent geometry : bond 0.00254 (15484) covalent geometry : angle 0.55040 (21042) *********************** 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 429 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 406 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: A 453 VAL cc_start: 0.8669 (t) cc_final: 0.8438 (m) REVERT: A 460 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7716 (ttm-80) REVERT: A 509 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7599 (mmm160) REVERT: A 525 LYS cc_start: 0.7653 (tttp) cc_final: 0.7314 (ttpp) REVERT: B 509 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7545 (mmm-85) REVERT: C 454 GLU cc_start: 0.8547 (tt0) cc_final: 0.8296 (tt0) REVERT: C 456 MET cc_start: 0.8456 (mmm) cc_final: 0.8201 (mpp) REVERT: C 460 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7705 (ttm-80) REVERT: C 509 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7527 (mmt90) REVERT: D 454 GLU cc_start: 0.8595 (tt0) cc_final: 0.8303 (tt0) REVERT: E 423 GLU cc_start: 0.7873 (pt0) cc_final: 0.7520 (pt0) REVERT: E 460 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7738 (ttt-90) REVERT: E 509 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7600 (mmm160) REVERT: F 423 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: F 460 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: F 509 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7705 (mmp80) REVERT: G 423 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: G 454 GLU cc_start: 0.8436 (tt0) cc_final: 0.8149 (tt0) REVERT: H 423 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: H 453 VAL cc_start: 0.8674 (t) cc_final: 0.8443 (m) REVERT: H 460 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: H 509 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7602 (mmm160) REVERT: H 525 LYS cc_start: 0.7647 (tttp) cc_final: 0.7306 (ttpp) REVERT: I 423 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: I 460 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7753 (ttm-80) REVERT: J 454 GLU cc_start: 0.8544 (tt0) cc_final: 0.8290 (tt0) REVERT: J 456 MET cc_start: 0.8469 (mmm) cc_final: 0.8218 (mpp) REVERT: J 460 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: J 509 ARG cc_start: 0.7833 (mmp-170) cc_final: 0.7429 (mmp80) REVERT: K 454 GLU cc_start: 0.8605 (tt0) cc_final: 0.8311 (tt0) REVERT: K 460 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: L 413 GLU cc_start: 0.7928 (pt0) cc_final: 0.7635 (pt0) REVERT: L 423 GLU cc_start: 0.7883 (pt0) cc_final: 0.7537 (pt0) REVERT: L 509 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7610 (mmm160) REVERT: M 423 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: M 460 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7667 (ttm-80) REVERT: N 423 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: N 454 GLU cc_start: 0.8418 (tt0) cc_final: 0.8125 (tt0) outliers start: 23 outliers final: 4 residues processed: 406 average time/residue: 3.1935 time to fit residues: 1405.2025 Evaluate side-chains 417 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 401 time to evaluate : 2.496 ------------------------------------------------------------------------------- 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 I residue 423 GLU Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain K 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 3 optimal weight: 0.0770 chunk 181 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 163 optimal weight: 0.0770 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN B 412 GLN D 412 GLN D 528 ASN F 528 ASN H 528 ASN I 412 GLN K 528 ASN M 528 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144622 restraints weight = 41188.860| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.61 r_work: 0.3546 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15484 Z= 0.101 Angle : 0.506 3.938 21042 Z= 0.272 Chirality : 0.044 0.149 2240 Planarity : 0.006 0.077 2814 Dihedral : 4.992 26.271 2044 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.06 % Allowed : 9.19 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1862 helix: 0.46 (0.22), residues: 476 sheet: 2.49 (0.22), residues: 686 loop : -0.39 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 519 HIS 0.002 0.001 HIS J 475 PHE 0.009 0.001 PHE M 444 TYR 0.003 0.001 TYR C 462 ARG 0.003 0.000 ARG L 507 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 658) hydrogen bonds : angle 4.30345 ( 1806) covalent geometry : bond 0.00207 (15484) covalent geometry : angle 0.50629 (21042) *********************** 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: 17 poor density : 400 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: A 453 VAL cc_start: 0.8661 (t) cc_final: 0.8446 (m) REVERT: A 460 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7689 (ttm-80) REVERT: A 509 ARG cc_start: 0.7823 (mmp80) cc_final: 0.7597 (mmm160) REVERT: A 525 LYS cc_start: 0.7566 (tttp) cc_final: 0.7239 (ttpp) REVERT: B 423 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: B 509 ARG cc_start: 0.7799 (mmm160) cc_final: 0.7550 (mmm-85) REVERT: C 454 GLU cc_start: 0.8492 (tt0) cc_final: 0.8279 (tt0) REVERT: C 460 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7425 (ttp-110) REVERT: C 509 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7521 (mmt90) REVERT: D 454 GLU cc_start: 0.8515 (tt0) cc_final: 0.8219 (tt0) REVERT: E 413 GLU cc_start: 0.7794 (pt0) cc_final: 0.7535 (pt0) REVERT: E 423 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: E 460 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7807 (ttt-90) REVERT: E 509 ARG cc_start: 0.7770 (mmp80) cc_final: 0.7568 (mmm160) REVERT: F 460 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7725 (ttm-80) REVERT: F 509 ARG cc_start: 0.7862 (mmp80) cc_final: 0.7627 (mmm160) REVERT: G 454 GLU cc_start: 0.8414 (tt0) cc_final: 0.8081 (tt0) REVERT: H 423 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: H 453 VAL cc_start: 0.8668 (t) cc_final: 0.8446 (m) REVERT: H 460 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7657 (ttm-80) REVERT: H 509 ARG cc_start: 0.7811 (mmp80) cc_final: 0.7584 (mmm160) REVERT: H 525 LYS cc_start: 0.7554 (tttp) cc_final: 0.7222 (ttpp) REVERT: I 423 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: I 460 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7722 (ttm-80) REVERT: J 454 GLU cc_start: 0.8487 (tt0) cc_final: 0.8230 (tt0) REVERT: J 460 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7669 (ttm-80) REVERT: J 509 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7405 (mmp80) REVERT: K 454 GLU cc_start: 0.8554 (tt0) cc_final: 0.8257 (tt0) REVERT: L 413 GLU cc_start: 0.7908 (pt0) cc_final: 0.7581 (pt0) REVERT: L 423 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: N 454 GLU cc_start: 0.8420 (tt0) cc_final: 0.8084 (tt0) outliers start: 17 outliers final: 3 residues processed: 400 average time/residue: 3.2515 time to fit residues: 1407.7227 Evaluate side-chains 405 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 394 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 423 GLU 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 H residue 423 GLU Chi-restraints excluded: chain I residue 423 GLU Chi-restraints excluded: chain J residue 423 GLU Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain L residue 423 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 56 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN A 500 GLN B 412 GLN B 500 GLN E 412 GLN H 412 GLN I 412 GLN J 500 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144383 restraints weight = 41607.959| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.59 r_work: 0.3559 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3715 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= 0.189 Angle : 0.616 6.499 21042 Z= 0.338 Chirality : 0.046 0.151 2240 Planarity : 0.007 0.073 2814 Dihedral : 5.202 27.412 2044 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.30 % Allowed : 10.25 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1862 helix: 0.21 (0.22), residues: 476 sheet: 2.60 (0.22), residues: 686 loop : -0.52 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 519 HIS 0.004 0.001 HIS C 532 PHE 0.012 0.002 PHE L 444 TYR 0.007 0.002 TYR E 462 ARG 0.007 0.001 ARG A 507 Details of bonding type rmsd hydrogen bonds : bond 0.05919 ( 658) hydrogen bonds : angle 4.61022 ( 1806) covalent geometry : bond 0.00421 (15484) covalent geometry : angle 0.61602 (21042) *********************** 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 407 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 386 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7731 (ttm-80) REVERT: A 509 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7597 (mmm160) REVERT: A 525 LYS cc_start: 0.7640 (tttp) cc_final: 0.7283 (ttpp) REVERT: B 423 GLU cc_start: 0.7958 (pt0) cc_final: 0.7670 (pt0) REVERT: C 454 GLU cc_start: 0.8568 (tt0) cc_final: 0.8341 (tt0) REVERT: C 460 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7680 (ttm-80) REVERT: C 509 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7483 (mmp80) REVERT: D 454 GLU cc_start: 0.8602 (tt0) cc_final: 0.8318 (tt0) REVERT: E 423 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: E 460 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7761 (ttt-90) REVERT: F 460 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: G 454 GLU cc_start: 0.8549 (tt0) cc_final: 0.8221 (tt0) REVERT: H 460 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7717 (ttm-80) REVERT: H 509 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7600 (mmm160) REVERT: H 525 LYS cc_start: 0.7632 (tttp) cc_final: 0.7282 (ttpp) REVERT: I 423 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: I 460 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: I 509 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7233 (mmp80) REVERT: J 454 GLU cc_start: 0.8595 (tt0) cc_final: 0.8369 (tt0) REVERT: J 460 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7650 (ttm-80) REVERT: J 509 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7390 (mmp80) REVERT: K 454 GLU cc_start: 0.8615 (tt0) cc_final: 0.8327 (tt0) REVERT: L 423 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7541 (pt0) REVERT: N 454 GLU cc_start: 0.8538 (tt0) cc_final: 0.8218 (tt0) outliers start: 21 outliers final: 6 residues processed: 386 average time/residue: 3.3837 time to fit residues: 1412.3770 Evaluate side-chains 393 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 379 time to evaluate : 2.196 ------------------------------------------------------------------------------- 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 H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 423 GLU 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 L residue 423 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN E 412 GLN I 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 = 0.3944 r_free = 0.3944 target = 0.171925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143064 restraints weight = 41482.238| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.62 r_work: 0.3546 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15484 Z= 0.178 Angle : 0.615 6.812 21042 Z= 0.338 Chirality : 0.046 0.154 2240 Planarity : 0.007 0.081 2814 Dihedral : 5.315 29.052 2044 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.43 % Allowed : 10.37 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1862 helix: 0.09 (0.22), residues: 476 sheet: 2.59 (0.22), residues: 686 loop : -0.60 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 519 HIS 0.003 0.001 HIS I 484 PHE 0.011 0.002 PHE L 444 TYR 0.008 0.002 TYR A 462 ARG 0.006 0.001 ARG A 507 Details of bonding type rmsd hydrogen bonds : bond 0.05922 ( 658) hydrogen bonds : angle 4.67583 ( 1806) covalent geometry : bond 0.00386 (15484) covalent geometry : angle 0.61517 (21042) *********************** 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 411 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 388 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: A 509 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7579 (mmm160) REVERT: A 525 LYS cc_start: 0.7660 (tttp) cc_final: 0.7291 (ttpp) REVERT: B 420 GLN cc_start: 0.8387 (mt0) cc_final: 0.8093 (mt0) REVERT: B 423 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: C 454 GLU cc_start: 0.8582 (tt0) cc_final: 0.8344 (tt0) REVERT: C 460 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7687 (ttm-80) REVERT: C 509 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7515 (mmp80) REVERT: D 454 GLU cc_start: 0.8620 (tt0) cc_final: 0.8289 (tt0) REVERT: E 423 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: E 460 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7766 (ttm-80) REVERT: F 460 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7710 (ttm-80) REVERT: G 454 GLU cc_start: 0.8619 (tt0) cc_final: 0.8275 (tt0) REVERT: H 460 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7734 (ttm-80) REVERT: H 509 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7588 (mmm160) REVERT: H 525 LYS cc_start: 0.7654 (tttp) cc_final: 0.7294 (ttpp) REVERT: I 420 GLN cc_start: 0.8397 (mt0) cc_final: 0.8107 (mt0) REVERT: I 423 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: I 460 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7709 (ttm-80) REVERT: I 509 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7256 (mmp80) REVERT: J 454 GLU cc_start: 0.8610 (tt0) cc_final: 0.8367 (tt0) REVERT: J 460 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7662 (ttm-80) REVERT: J 509 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7430 (mmp80) REVERT: K 454 GLU cc_start: 0.8633 (tt0) cc_final: 0.8304 (tt0) REVERT: L 413 GLU cc_start: 0.7996 (pt0) cc_final: 0.7700 (pt0) REVERT: L 423 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: N 454 GLU cc_start: 0.8603 (tt0) cc_final: 0.8250 (tt0) outliers start: 23 outliers final: 7 residues processed: 388 average time/residue: 3.2985 time to fit residues: 1383.9723 Evaluate side-chains 394 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 378 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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 423 GLU 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 E residue 423 GLU 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 423 GLU 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 L residue 423 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.172393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143665 restraints weight = 41640.508| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.62 r_work: 0.3552 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3846 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= 0.158 Angle : 0.585 6.183 21042 Z= 0.322 Chirality : 0.045 0.153 2240 Planarity : 0.007 0.082 2814 Dihedral : 5.270 29.401 2044 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.68 % Allowed : 10.75 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1862 helix: 0.17 (0.22), residues: 476 sheet: 2.57 (0.22), residues: 686 loop : -0.54 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 519 HIS 0.003 0.001 HIS B 484 PHE 0.010 0.002 PHE F 444 TYR 0.007 0.002 TYR A 462 ARG 0.005 0.001 ARG H 507 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 658) hydrogen bonds : angle 4.58170 ( 1806) covalent geometry : bond 0.00340 (15484) covalent geometry : angle 0.58537 (21042) *********************** 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 407 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 380 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: A 509 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7589 (mmm160) REVERT: A 525 LYS cc_start: 0.7659 (tttp) cc_final: 0.7290 (ttpp) REVERT: B 420 GLN cc_start: 0.8395 (mt0) cc_final: 0.8104 (mt0) REVERT: B 423 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: C 454 GLU cc_start: 0.8580 (tt0) cc_final: 0.8337 (tt0) REVERT: C 460 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: C 509 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7498 (mmt90) REVERT: D 454 GLU cc_start: 0.8610 (tt0) cc_final: 0.8282 (tt0) REVERT: D 521 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7568 (ttp80) REVERT: E 423 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: E 460 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7757 (ttm-80) REVERT: E 474 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8686 (mp) REVERT: F 460 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7702 (ttm-80) REVERT: G 454 GLU cc_start: 0.8594 (tt0) cc_final: 0.8234 (tt0) REVERT: H 460 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7743 (ttm-80) REVERT: H 509 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7579 (mmm160) REVERT: H 525 LYS cc_start: 0.7664 (tttp) cc_final: 0.7305 (ttpp) REVERT: I 420 GLN cc_start: 0.8397 (mt0) cc_final: 0.8108 (mt0) REVERT: I 423 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: I 460 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7724 (ttm-80) REVERT: I 509 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7656 (mmm160) REVERT: J 454 GLU cc_start: 0.8613 (tt0) cc_final: 0.8387 (tt0) REVERT: J 460 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7666 (ttm-80) REVERT: J 509 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7408 (mmp80) REVERT: K 423 GLU cc_start: 0.7905 (pt0) cc_final: 0.7531 (pt0) REVERT: K 454 GLU cc_start: 0.8626 (tt0) cc_final: 0.8297 (tt0) REVERT: K 521 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7579 (ttp80) REVERT: L 423 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: L 474 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8679 (mp) REVERT: N 454 GLU cc_start: 0.8609 (tt0) cc_final: 0.8257 (tt0) outliers start: 27 outliers final: 7 residues processed: 383 average time/residue: 3.2646 time to fit residues: 1352.9227 Evaluate side-chains 404 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 384 time to evaluate : 2.226 ------------------------------------------------------------------------------- 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 423 GLU 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 423 GLU 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 423 GLU Chi-restraints excluded: chain L residue 474 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 172 optimal weight: 0.0050 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.172047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143310 restraints weight = 41554.988| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.62 r_work: 0.3548 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 15484 Z= 0.169 Angle : 0.602 6.608 21042 Z= 0.331 Chirality : 0.045 0.154 2240 Planarity : 0.007 0.083 2814 Dihedral : 5.296 29.730 2044 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.24 % Allowed : 11.49 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1862 helix: 0.17 (0.22), residues: 476 sheet: 2.59 (0.23), residues: 686 loop : -0.58 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 519 HIS 0.004 0.001 HIS B 484 PHE 0.011 0.002 PHE D 444 TYR 0.008 0.002 TYR A 462 ARG 0.005 0.001 ARG A 507 Details of bonding type rmsd hydrogen bonds : bond 0.05741 ( 658) hydrogen bonds : angle 4.62160 ( 1806) covalent geometry : bond 0.00364 (15484) covalent geometry : angle 0.60194 (21042) *********************** 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 395 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 375 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7758 (ttm-80) REVERT: A 509 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7588 (mmm160) REVERT: A 525 LYS cc_start: 0.7655 (tttp) cc_final: 0.7296 (ttpp) REVERT: B 420 GLN cc_start: 0.8405 (mt0) cc_final: 0.8119 (mt0) REVERT: B 423 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: C 454 GLU cc_start: 0.8584 (tt0) cc_final: 0.8361 (tt0) REVERT: C 460 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7684 (ttm-80) REVERT: C 509 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7516 (mmt90) REVERT: D 423 GLU cc_start: 0.7888 (pt0) cc_final: 0.7482 (pt0) REVERT: D 454 GLU cc_start: 0.8607 (tt0) cc_final: 0.8282 (tt0) REVERT: D 521 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7557 (ttp80) REVERT: E 423 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7570 (pt0) REVERT: E 460 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: E 474 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8716 (mp) REVERT: F 460 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7686 (ttm-80) REVERT: G 454 GLU cc_start: 0.8584 (tt0) cc_final: 0.8238 (tt0) REVERT: H 460 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7773 (ttm-80) REVERT: H 509 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7580 (mmm160) REVERT: H 525 LYS cc_start: 0.7653 (tttp) cc_final: 0.7297 (ttpp) REVERT: I 420 GLN cc_start: 0.8423 (mt0) cc_final: 0.8140 (mt0) REVERT: I 423 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: I 460 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: I 509 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7649 (mmm160) REVERT: J 454 GLU cc_start: 0.8601 (tt0) cc_final: 0.8359 (tt0) REVERT: J 460 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: J 509 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7377 (mmp80) REVERT: K 423 GLU cc_start: 0.7899 (pt0) cc_final: 0.7474 (pt0) REVERT: K 454 GLU cc_start: 0.8630 (tt0) cc_final: 0.8304 (tt0) REVERT: K 521 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7570 (ttp80) REVERT: L 413 GLU cc_start: 0.7977 (pt0) cc_final: 0.7712 (pt0) REVERT: L 423 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: L 474 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8717 (mp) REVERT: N 454 GLU cc_start: 0.8594 (tt0) cc_final: 0.8240 (tt0) outliers start: 20 outliers final: 5 residues processed: 375 average time/residue: 3.3423 time to fit residues: 1359.0249 Evaluate side-chains 395 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 377 time to evaluate : 2.325 ------------------------------------------------------------------------------- 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 423 GLU 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 H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 423 GLU Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I 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 423 GLU Chi-restraints excluded: chain L residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.174477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146055 restraints weight = 41350.173| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.61 r_work: 0.3584 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15484 Z= 0.118 Angle : 0.530 4.918 21042 Z= 0.289 Chirality : 0.044 0.146 2240 Planarity : 0.007 0.080 2814 Dihedral : 5.116 29.511 2044 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.12 % Allowed : 11.68 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1862 helix: 0.11 (0.22), residues: 504 sheet: 2.55 (0.23), residues: 686 loop : -0.32 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 519 HIS 0.003 0.001 HIS J 459 PHE 0.009 0.001 PHE F 444 TYR 0.005 0.001 TYR A 462 ARG 0.005 0.000 ARG H 507 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 658) hydrogen bonds : angle 4.35291 ( 1806) covalent geometry : bond 0.00243 (15484) covalent geometry : angle 0.53018 (21042) ********************** 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 405 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 387 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7750 (ttm-80) REVERT: A 509 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7570 (mmm160) REVERT: A 525 LYS cc_start: 0.7610 (tttp) cc_final: 0.7256 (ttpp) REVERT: B 420 GLN cc_start: 0.8352 (mt0) cc_final: 0.8061 (mt0) REVERT: B 423 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: B 485 VAL cc_start: 0.8244 (t) cc_final: 0.7955 (t) REVERT: C 454 GLU cc_start: 0.8517 (tt0) cc_final: 0.8291 (tt0) REVERT: C 460 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7416 (ttp-110) REVERT: C 509 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7475 (mmt90) REVERT: D 423 GLU cc_start: 0.7865 (pt0) cc_final: 0.7483 (pt0) REVERT: D 454 GLU cc_start: 0.8576 (tt0) cc_final: 0.8287 (tt0) REVERT: D 521 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7538 (ttp80) REVERT: E 423 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: E 460 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7748 (ttm-80) REVERT: E 474 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8706 (mp) REVERT: E 509 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7573 (mmm160) REVERT: F 460 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7695 (ttm-80) REVERT: G 454 GLU cc_start: 0.8525 (tt0) cc_final: 0.8172 (tt0) REVERT: H 460 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: H 509 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7566 (mmm160) REVERT: H 525 LYS cc_start: 0.7610 (tttp) cc_final: 0.7262 (ttpp) REVERT: I 423 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: I 460 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: I 485 VAL cc_start: 0.8269 (t) cc_final: 0.7968 (t) REVERT: J 454 GLU cc_start: 0.8544 (tt0) cc_final: 0.8325 (tt0) REVERT: J 460 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7665 (ttm-80) REVERT: J 509 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7371 (mmp80) REVERT: K 423 GLU cc_start: 0.7846 (pt0) cc_final: 0.7437 (pt0) REVERT: K 454 GLU cc_start: 0.8579 (tt0) cc_final: 0.8284 (tt0) REVERT: K 521 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7551 (ttp80) REVERT: L 413 GLU cc_start: 0.7828 (pt0) cc_final: 0.7571 (pt0) REVERT: L 423 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: L 474 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8701 (mp) REVERT: N 454 GLU cc_start: 0.8549 (tt0) cc_final: 0.8203 (tt0) outliers start: 18 outliers final: 4 residues processed: 387 average time/residue: 3.2842 time to fit residues: 1375.4397 Evaluate side-chains 402 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 385 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 423 GLU 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 H residue 423 GLU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 423 GLU Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 521 ARG Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain L residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 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 = 0.3960 r_free = 0.3960 target = 0.173630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.144775 restraints weight = 41265.685| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.64 r_work: 0.3567 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3963 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 : 0.557 5.559 21042 Z= 0.303 Chirality : 0.045 0.148 2240 Planarity : 0.007 0.079 2814 Dihedral : 5.100 28.980 2044 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.12 % Allowed : 11.80 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1862 helix: 0.10 (0.22), residues: 504 sheet: 2.59 (0.23), residues: 686 loop : -0.34 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 519 HIS 0.003 0.001 HIS B 484 PHE 0.010 0.001 PHE M 444 TYR 0.007 0.001 TYR A 462 ARG 0.009 0.001 ARG L 507 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 658) hydrogen bonds : angle 4.38491 ( 1806) covalent geometry : bond 0.00296 (15484) covalent geometry : angle 0.55741 (21042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26452.28 seconds wall clock time: 451 minutes 50.23 seconds (27110.23 seconds total)