Starting phenix.real_space_refine on Wed Jun 25 09:28:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6k_41070/06_2025/8t6k_41070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6k_41070/06_2025/8t6k_41070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6k_41070/06_2025/8t6k_41070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6k_41070/06_2025/8t6k_41070.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6k_41070/06_2025/8t6k_41070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6k_41070/06_2025/8t6k_41070.cif" } resolution = 3.0 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= 0.030 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 9534 2.51 5 N 2702 2.21 5 O 2814 1.98 5 H 14616 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29722 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 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: 7.74, per 1000 atoms: 0.26 Number of scatterers: 29722 At special positions: 0 Unit cell: (140.18, 135.88, 69.66, 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 2814 8.00 N 2702 7.00 C 9534 6.00 H 14616 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: 6.95 Conformation dependent library (CDL) restraints added in 2.3 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: 84 helices and 14 sheets defined 38.6% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 408 through 428 removed outlier: 4.210A pdb=" N GLN A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 463 " --> pdb=" O HIS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'B' and resid 409 through 428 removed outlier: 3.762A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 463 " --> pdb=" O HIS B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 522 through 525 Processing helix chain 'C' and resid 409 through 428 removed outlier: 3.762A pdb=" N GLU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 449 Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 463 " --> pdb=" O HIS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 470 Processing helix chain 'C' and resid 522 through 525 Processing helix chain 'D' and resid 409 through 428 removed outlier: 3.762A pdb=" N GLU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 449 Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.930A pdb=" N PHE D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 463 " --> pdb=" O HIS D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 470 Processing helix chain 'D' and resid 522 through 525 Processing helix chain 'E' and resid 409 through 428 removed outlier: 3.761A pdb=" N GLU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 449 Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR E 462 " --> pdb=" O PHE E 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 463 " --> pdb=" O HIS E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 470 Processing helix chain 'E' and resid 522 through 525 Processing helix chain 'F' and resid 409 through 428 removed outlier: 3.762A pdb=" N GLU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR F 462 " --> pdb=" O PHE F 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE F 463 " --> pdb=" O HIS F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 470 Processing helix chain 'F' and resid 522 through 525 Processing helix chain 'G' and resid 409 through 428 removed outlier: 3.761A pdb=" N GLU G 413 " --> pdb=" O ALA G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS G 435 " --> pdb=" O GLU G 431 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE G 436 " --> pdb=" O ALA G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 449 Processing helix chain 'G' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE G 461 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR G 462 " --> pdb=" O PHE G 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE G 463 " --> pdb=" O HIS G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 470 Processing helix chain 'G' and resid 522 through 525 Processing helix chain 'H' and resid 409 through 428 removed outlier: 3.762A pdb=" N GLU H 413 " --> pdb=" O ALA H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS H 435 " --> pdb=" O GLU H 431 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE H 436 " --> pdb=" O ALA H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 449 Processing helix chain 'H' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE H 461 " --> pdb=" O ASP H 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR H 462 " --> pdb=" O PHE H 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE H 463 " --> pdb=" O HIS H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 467 through 470 Processing helix chain 'H' and resid 522 through 525 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.762A pdb=" N GLU I 413 " --> pdb=" O ALA I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS I 435 " --> pdb=" O GLU I 431 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE I 436 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 449 Processing helix chain 'I' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE I 461 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR I 462 " --> pdb=" O PHE I 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE I 463 " --> pdb=" O HIS I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 467 through 470 Processing helix chain 'I' and resid 522 through 525 Processing helix chain 'J' and resid 409 through 428 removed outlier: 3.761A pdb=" N GLU J 413 " --> pdb=" O ALA J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS J 435 " --> pdb=" O GLU J 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE J 436 " --> pdb=" O ALA J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 449 Processing helix chain 'J' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE J 461 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR J 462 " --> pdb=" O PHE J 458 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE J 463 " --> pdb=" O HIS J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 470 Processing helix chain 'J' and resid 522 through 525 Processing helix chain 'K' and resid 409 through 428 removed outlier: 3.761A pdb=" N GLU K 413 " --> pdb=" O ALA K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS K 435 " --> pdb=" O GLU K 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE K 436 " --> pdb=" O ALA K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 449 Processing helix chain 'K' and resid 456 through 466 removed outlier: 3.930A pdb=" N PHE K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR K 462 " --> pdb=" O PHE K 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE K 463 " --> pdb=" O HIS K 459 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 470 Processing helix chain 'K' and resid 522 through 525 Processing helix chain 'L' and resid 409 through 428 removed outlier: 3.761A pdb=" N GLU L 413 " --> pdb=" O ALA L 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS L 435 " --> pdb=" O GLU L 431 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE L 436 " --> pdb=" O ALA L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 449 Processing helix chain 'L' and resid 456 through 466 removed outlier: 3.930A pdb=" N PHE L 461 " --> pdb=" O ASP L 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR L 462 " --> pdb=" O PHE L 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE L 463 " --> pdb=" O HIS L 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 470 Processing helix chain 'L' and resid 522 through 525 Processing helix chain 'M' and resid 409 through 428 removed outlier: 3.762A pdb=" N GLU M 413 " --> pdb=" O ALA M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS M 435 " --> pdb=" O GLU M 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE M 436 " --> pdb=" O ALA M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 449 Processing helix chain 'M' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE M 461 " --> pdb=" O ASP M 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR M 462 " --> pdb=" O PHE M 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE M 463 " --> pdb=" O HIS M 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 470 Processing helix chain 'M' and resid 522 through 525 Processing helix chain 'N' and resid 409 through 428 removed outlier: 3.761A pdb=" N GLU N 413 " --> pdb=" O ALA N 409 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 436 removed outlier: 3.678A pdb=" N LYS N 435 " --> pdb=" O GLU N 431 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE N 436 " --> pdb=" O ALA N 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 449 Processing helix chain 'N' and resid 456 through 466 removed outlier: 3.931A pdb=" N PHE N 461 " --> pdb=" O ASP N 457 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR N 462 " --> pdb=" O PHE N 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE N 463 " --> pdb=" O HIS N 459 " (cutoff:3.500A) Processing helix chain 'N' and resid 467 through 470 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: 5.418A pdb=" N ASP A 438 " --> pdb=" O GLN A 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 529 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY A 440 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE A 531 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 442 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N CYS A 533 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE A 444 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY A 535 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 518 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A 531 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A 516 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS A 533 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU A 514 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY A 535 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN A 512 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA A 490 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL A 485 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS A 492 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 483 " --> pdb=" O CYS A 492 " (cutoff:3.500A) removed outlier: 6.657A 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: 5.418A pdb=" N ASP B 438 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 529 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY B 440 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE B 531 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR B 442 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N CYS B 533 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE B 444 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY B 535 " --> pdb=" O PHE B 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 518 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE B 531 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR B 516 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS B 533 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU B 514 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY B 535 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN B 512 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA B 490 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 485 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS B 492 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 483 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 6.656A 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: 5.418A pdb=" N ASP C 438 " --> pdb=" O GLN C 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 529 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY C 440 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE C 531 " --> pdb=" O GLY C 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 442 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N CYS C 533 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE C 444 " --> pdb=" O CYS C 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY C 535 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 518 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE C 531 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR C 516 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N CYS C 533 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 514 " --> pdb=" O CYS C 533 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY C 535 " --> pdb=" O GLN C 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN C 512 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA C 490 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL C 485 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS C 492 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 483 " --> pdb=" O CYS C 492 " (cutoff:3.500A) removed outlier: 6.658A 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: 5.418A pdb=" N ASP D 438 " --> pdb=" O GLN D 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 529 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY D 440 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE D 531 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR D 442 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS D 533 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE D 444 " --> pdb=" O CYS D 533 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLY D 535 " --> pdb=" O PHE D 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL D 518 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE D 531 " --> pdb=" O THR D 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR D 516 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N CYS D 533 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU D 514 " --> pdb=" O CYS D 533 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY D 535 " --> pdb=" O GLN D 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN D 512 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA D 490 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL D 485 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS D 492 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 483 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 6.656A 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: 5.418A pdb=" N ASP E 438 " --> pdb=" O GLN E 527 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL E 529 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY E 440 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE E 531 " --> pdb=" O GLY E 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 442 " --> pdb=" O PHE E 531 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS E 533 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE E 444 " --> pdb=" O CYS E 533 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLY E 535 " --> pdb=" O PHE E 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL E 518 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE E 531 " --> pdb=" O THR E 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR E 516 " --> pdb=" O PHE E 531 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N CYS E 533 " --> pdb=" O GLU E 514 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU E 514 " --> pdb=" O CYS E 533 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY E 535 " --> pdb=" O GLN E 512 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLN E 512 " --> pdb=" O GLY E 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA E 490 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL E 485 " --> pdb=" O ALA E 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS E 492 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL E 483 " --> pdb=" O CYS E 492 " (cutoff:3.500A) removed outlier: 6.656A 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: 5.418A pdb=" N ASP F 438 " --> pdb=" O GLN F 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL F 529 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY F 440 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE F 531 " --> pdb=" O GLY F 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR F 442 " --> pdb=" O PHE F 531 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N CYS F 533 " --> pdb=" O THR F 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE F 444 " --> pdb=" O CYS F 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY F 535 " --> pdb=" O PHE F 444 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL F 518 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE F 531 " --> pdb=" O THR F 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR F 516 " --> pdb=" O PHE F 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS F 533 " --> pdb=" O GLU F 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU F 514 " --> pdb=" O CYS F 533 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY F 535 " --> pdb=" O GLN F 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN F 512 " --> pdb=" O GLY F 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA F 490 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL F 485 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS F 492 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL F 483 " --> pdb=" O CYS F 492 " (cutoff:3.500A) removed outlier: 6.657A 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: 5.418A pdb=" N ASP G 438 " --> pdb=" O GLN G 527 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL G 529 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY G 440 " --> pdb=" O VAL G 529 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE G 531 " --> pdb=" O GLY G 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR G 442 " --> pdb=" O PHE G 531 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS G 533 " --> pdb=" O THR G 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE G 444 " --> pdb=" O CYS G 533 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY G 535 " --> pdb=" O PHE G 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL G 518 " --> pdb=" O VAL G 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE G 531 " --> pdb=" O THR G 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR G 516 " --> pdb=" O PHE G 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS G 533 " --> pdb=" O GLU G 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU G 514 " --> pdb=" O CYS G 533 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY G 535 " --> pdb=" O GLN G 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN G 512 " --> pdb=" O GLY G 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA G 490 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL G 485 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS G 492 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL G 483 " --> pdb=" O CYS G 492 " (cutoff:3.500A) removed outlier: 6.657A 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: 5.418A pdb=" N ASP H 438 " --> pdb=" O GLN H 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL H 529 " --> pdb=" O ASP H 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY H 440 " --> pdb=" O VAL H 529 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE H 531 " --> pdb=" O GLY H 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR H 442 " --> pdb=" O PHE H 531 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N CYS H 533 " --> pdb=" O THR H 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE H 444 " --> pdb=" O CYS H 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY H 535 " --> pdb=" O PHE H 444 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL H 518 " --> pdb=" O VAL H 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE H 531 " --> pdb=" O THR H 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR H 516 " --> pdb=" O PHE H 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS H 533 " --> pdb=" O GLU H 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU H 514 " --> pdb=" O CYS H 533 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY H 535 " --> pdb=" O GLN H 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN H 512 " --> pdb=" O GLY H 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA H 490 " --> pdb=" O VAL H 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL H 485 " --> pdb=" O ALA H 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS H 492 " --> pdb=" O VAL H 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL H 483 " --> pdb=" O CYS H 492 " (cutoff:3.500A) removed outlier: 6.657A 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: 5.419A pdb=" N ASP I 438 " --> pdb=" O GLN I 527 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL I 529 " --> pdb=" O ASP I 438 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY I 440 " --> pdb=" O VAL I 529 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE I 531 " --> pdb=" O GLY I 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR I 442 " --> pdb=" O PHE I 531 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N CYS I 533 " --> pdb=" O THR I 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE I 444 " --> pdb=" O CYS I 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY I 535 " --> pdb=" O PHE I 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL I 518 " --> pdb=" O VAL I 529 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE I 531 " --> pdb=" O THR I 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR I 516 " --> pdb=" O PHE I 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS I 533 " --> pdb=" O GLU I 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU I 514 " --> pdb=" O CYS I 533 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY I 535 " --> pdb=" O GLN I 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN I 512 " --> pdb=" O GLY I 535 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA I 490 " --> pdb=" O VAL I 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL I 485 " --> pdb=" O ALA I 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS I 492 " --> pdb=" O VAL I 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL I 483 " --> pdb=" O CYS I 492 " (cutoff:3.500A) removed outlier: 6.656A 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: 5.419A pdb=" N ASP J 438 " --> pdb=" O GLN J 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL J 529 " --> pdb=" O ASP J 438 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY J 440 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE J 531 " --> pdb=" O GLY J 440 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR J 442 " --> pdb=" O PHE J 531 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N CYS J 533 " --> pdb=" O THR J 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE J 444 " --> pdb=" O CYS J 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY J 535 " --> pdb=" O PHE J 444 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL J 518 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE J 531 " --> pdb=" O THR J 516 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR J 516 " --> pdb=" O PHE J 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS J 533 " --> pdb=" O GLU J 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU J 514 " --> pdb=" O CYS J 533 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY J 535 " --> pdb=" O GLN J 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN J 512 " --> pdb=" O GLY J 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA J 490 " --> pdb=" O VAL J 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL J 485 " --> pdb=" O ALA J 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS J 492 " --> pdb=" O VAL J 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL J 483 " --> pdb=" O CYS J 492 " (cutoff:3.500A) removed outlier: 6.656A 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: 5.418A pdb=" N ASP K 438 " --> pdb=" O GLN K 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL K 529 " --> pdb=" O ASP K 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY K 440 " --> pdb=" O VAL K 529 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE K 531 " --> pdb=" O GLY K 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR K 442 " --> pdb=" O PHE K 531 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS K 533 " --> pdb=" O THR K 442 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE K 444 " --> pdb=" O CYS K 533 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLY K 535 " --> pdb=" O PHE K 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL K 518 " --> pdb=" O VAL K 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE K 531 " --> pdb=" O THR K 516 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR K 516 " --> pdb=" O PHE K 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS K 533 " --> pdb=" O GLU K 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU K 514 " --> pdb=" O CYS K 533 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY K 535 " --> pdb=" O GLN K 512 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLN K 512 " --> pdb=" O GLY K 535 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA K 490 " --> pdb=" O VAL K 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL K 485 " --> pdb=" O ALA K 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS K 492 " --> pdb=" O VAL K 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL K 483 " --> pdb=" O CYS K 492 " (cutoff:3.500A) removed outlier: 6.657A 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: 5.418A pdb=" N ASP L 438 " --> pdb=" O GLN L 527 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL L 529 " --> pdb=" O ASP L 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY L 440 " --> pdb=" O VAL L 529 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE L 531 " --> pdb=" O GLY L 440 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR L 442 " --> pdb=" O PHE L 531 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS L 533 " --> pdb=" O THR L 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE L 444 " --> pdb=" O CYS L 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY L 535 " --> pdb=" O PHE L 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL L 518 " --> pdb=" O VAL L 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE L 531 " --> pdb=" O THR L 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR L 516 " --> pdb=" O PHE L 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS L 533 " --> pdb=" O GLU L 514 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU L 514 " --> pdb=" O CYS L 533 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY L 535 " --> pdb=" O GLN L 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN L 512 " --> pdb=" O GLY L 535 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA L 490 " --> pdb=" O VAL L 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL L 485 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS L 492 " --> pdb=" O VAL L 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL L 483 " --> pdb=" O CYS L 492 " (cutoff:3.500A) removed outlier: 6.657A 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: 5.418A pdb=" N ASP M 438 " --> pdb=" O GLN M 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL M 529 " --> pdb=" O ASP M 438 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY M 440 " --> pdb=" O VAL M 529 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE M 531 " --> pdb=" O GLY M 440 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR M 442 " --> pdb=" O PHE M 531 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N CYS M 533 " --> pdb=" O THR M 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE M 444 " --> pdb=" O CYS M 533 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY M 535 " --> pdb=" O PHE M 444 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL M 518 " --> pdb=" O VAL M 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE M 531 " --> pdb=" O THR M 516 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR M 516 " --> pdb=" O PHE M 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS M 533 " --> pdb=" O GLU M 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU M 514 " --> pdb=" O CYS M 533 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY M 535 " --> pdb=" O GLN M 512 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLN M 512 " --> pdb=" O GLY M 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA M 490 " --> pdb=" O VAL M 485 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL M 485 " --> pdb=" O ALA M 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS M 492 " --> pdb=" O VAL M 483 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL M 483 " --> pdb=" O CYS M 492 " (cutoff:3.500A) removed outlier: 6.657A 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: 5.418A pdb=" N ASP N 438 " --> pdb=" O GLN N 527 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL N 529 " --> pdb=" O ASP N 438 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY N 440 " --> pdb=" O VAL N 529 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE N 531 " --> pdb=" O GLY N 440 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR N 442 " --> pdb=" O PHE N 531 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS N 533 " --> pdb=" O THR N 442 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE N 444 " --> pdb=" O CYS N 533 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLY N 535 " --> pdb=" O PHE N 444 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL N 518 " --> pdb=" O VAL N 529 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE N 531 " --> pdb=" O THR N 516 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR N 516 " --> pdb=" O PHE N 531 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS N 533 " --> pdb=" O GLU N 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU N 514 " --> pdb=" O CYS N 533 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY N 535 " --> pdb=" O GLN N 512 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN N 512 " --> pdb=" O GLY N 535 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA N 490 " --> pdb=" O VAL N 485 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL N 485 " --> pdb=" O ALA N 490 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS N 492 " --> pdb=" O VAL N 483 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL N 483 " --> pdb=" O CYS N 492 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA N 494 " --> pdb=" O PRO N 481 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1764 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: 10.28 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 14574 1.13 - 1.30: 3010 1.30 - 1.47: 6493 1.47 - 1.65: 5967 1.65 - 1.82: 70 Bond restraints: 30114 Sorted by residual: bond pdb=" CA ASN D 480 " pdb=" CB ASN D 480 " ideal model delta sigma weight residual 1.522 1.459 0.063 7.00e-03 2.04e+04 8.07e+01 bond pdb=" CA ASN I 480 " pdb=" CB ASN I 480 " ideal model delta sigma weight residual 1.522 1.460 0.063 7.00e-03 2.04e+04 8.02e+01 bond pdb=" CA ASN N 480 " pdb=" CB ASN N 480 " ideal model delta sigma weight residual 1.522 1.460 0.063 7.00e-03 2.04e+04 8.01e+01 bond pdb=" CA ASN C 480 " pdb=" CB ASN C 480 " ideal model delta sigma weight residual 1.522 1.460 0.063 7.00e-03 2.04e+04 8.00e+01 bond pdb=" CA ASN K 480 " pdb=" CB ASN K 480 " ideal model delta sigma weight residual 1.522 1.460 0.063 7.00e-03 2.04e+04 7.99e+01 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 41749 2.49 - 4.99: 8656 4.99 - 7.48: 3199 7.48 - 9.98: 491 9.98 - 12.47: 239 Bond angle restraints: 54334 Sorted by residual: angle pdb=" CA ASN F 427 " pdb=" CB ASN F 427 " pdb=" CG ASN F 427 " ideal model delta sigma weight residual 112.60 120.30 -7.70 1.00e+00 1.00e+00 5.93e+01 angle pdb=" CA ASN C 427 " pdb=" CB ASN C 427 " pdb=" CG ASN C 427 " ideal model delta sigma weight residual 112.60 120.30 -7.70 1.00e+00 1.00e+00 5.93e+01 angle pdb=" CA ASN L 427 " pdb=" CB ASN L 427 " pdb=" CG ASN L 427 " ideal model delta sigma weight residual 112.60 120.29 -7.69 1.00e+00 1.00e+00 5.92e+01 angle pdb=" CA ASN B 427 " pdb=" CB ASN B 427 " pdb=" CG ASN B 427 " ideal model delta sigma weight residual 112.60 120.27 -7.67 1.00e+00 1.00e+00 5.89e+01 angle pdb=" CA ASN D 427 " pdb=" CB ASN D 427 " pdb=" CG ASN D 427 " ideal model delta sigma weight residual 112.60 120.27 -7.67 1.00e+00 1.00e+00 5.88e+01 ... (remaining 54329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 12712 15.63 - 31.26: 854 31.26 - 46.88: 336 46.88 - 62.51: 294 62.51 - 78.14: 70 Dihedral angle restraints: 14266 sinusoidal: 7700 harmonic: 6566 Sorted by residual: dihedral pdb=" CA SER M 534 " pdb=" C SER M 534 " pdb=" N GLY M 535 " pdb=" CA GLY M 535 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA SER B 534 " pdb=" C SER B 534 " pdb=" N GLY B 535 " pdb=" CA GLY B 535 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA SER I 534 " pdb=" C SER I 534 " pdb=" N GLY I 535 " pdb=" CA GLY I 535 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 14263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1761 0.144 - 0.288: 157 0.288 - 0.432: 14 0.432 - 0.576: 225 0.576 - 0.720: 83 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CG LEU K 467 " pdb=" CB LEU K 467 " pdb=" CD1 LEU K 467 " pdb=" CD2 LEU K 467 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CG LEU M 467 " pdb=" CB LEU M 467 " pdb=" CD1 LEU M 467 " pdb=" CD2 LEU M 467 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CG LEU F 467 " pdb=" CB LEU F 467 " pdb=" CD1 LEU F 467 " pdb=" CD2 LEU F 467 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 2237 not shown) Planarity restraints: 4564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 528 " 0.071 2.00e-02 2.50e+03 6.72e-02 6.77e+01 pdb=" CG ASN J 528 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN J 528 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN J 528 " -0.018 2.00e-02 2.50e+03 pdb="HD21 ASN J 528 " -0.079 2.00e-02 2.50e+03 pdb="HD22 ASN J 528 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 528 " -0.071 2.00e-02 2.50e+03 6.72e-02 6.77e+01 pdb=" CG ASN E 528 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN E 528 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN E 528 " 0.019 2.00e-02 2.50e+03 pdb="HD21 ASN E 528 " 0.078 2.00e-02 2.50e+03 pdb="HD22 ASN E 528 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 528 " 0.071 2.00e-02 2.50e+03 6.71e-02 6.75e+01 pdb=" CG ASN D 528 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 528 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN D 528 " -0.018 2.00e-02 2.50e+03 pdb="HD21 ASN D 528 " -0.078 2.00e-02 2.50e+03 pdb="HD22 ASN D 528 " 0.106 2.00e-02 2.50e+03 ... (remaining 4561 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2029 2.21 - 2.81: 51179 2.81 - 3.40: 75798 3.40 - 4.00: 104177 4.00 - 4.60: 152800 Nonbonded interactions: 385983 Sorted by model distance: nonbonded pdb=" HG SER J 443 " pdb=" OE2 GLU J 445 " model vdw 1.610 2.450 nonbonded pdb=" HG SER M 443 " pdb=" OE2 GLU M 445 " model vdw 1.610 2.450 nonbonded pdb=" HG SER F 443 " pdb=" OE2 GLU F 445 " model vdw 1.610 2.450 nonbonded pdb=" HG SER D 443 " pdb=" OE2 GLU D 445 " model vdw 1.610 2.450 nonbonded pdb=" HG SER L 443 " pdb=" OE2 GLU L 445 " model vdw 1.610 2.450 ... (remaining 385978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.500 Extract box with map and model: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 53.950 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.025 0.137 15498 Z= 1.389 Angle : 2.470 11.058 21042 Z= 1.580 Chirality : 0.223 0.720 2240 Planarity : 0.011 0.048 2800 Dihedral : 15.074 78.141 5712 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.74 % Allowed : 3.48 % Favored : 94.78 % Cbeta Deviations : 8.73 % 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: 1.56 (0.20), residues: 1862 helix: -1.36 (0.18), residues: 420 sheet: 3.70 (0.19), residues: 602 loop : 0.31 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.017 TRP G 519 HIS 0.003 0.001 HIS F 484 PHE 0.044 0.012 PHE K 444 TYR 0.090 0.022 TYR M 495 ARG 0.006 0.001 ARG K 410 Details of bonding type rmsd hydrogen bonds : bond 0.22245 ( 672) hydrogen bonds : angle 6.65214 ( 1764) covalent geometry : bond 0.02503 (15498) covalent geometry : angle 2.47027 (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 279 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 2.233 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: symmetry clash revert: symmetry clash REVERT: A 413 GLU cc_start: 0.6986 (pt0) cc_final: 0.6637 (pt0) REVERT: B 413 GLU cc_start: 0.7097 (pt0) cc_final: 0.6689 (pt0) REVERT: H 413 GLU cc_start: 0.7009 (pt0) cc_final: 0.6679 (pt0) REVERT: I 413 GLU cc_start: 0.6900 (pt0) cc_final: 0.6405 (pt0) outliers start: 28 outliers final: 2 residues processed: 251 average time/residue: 2.4787 time to fit residues: 691.6701 Evaluate side-chains 205 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain H residue 431 GLU 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: 0.9980 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 ASN D 465 ASN F 465 ASN J 465 ASN K 465 ASN M 465 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.184060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145478 restraints weight = 43341.779| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.16 r_work: 0.3344 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15498 Z= 0.148 Angle : 0.638 4.138 21042 Z= 0.348 Chirality : 0.042 0.122 2240 Planarity : 0.004 0.034 2800 Dihedral : 5.941 49.342 2050 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.25 % Allowed : 10.12 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.49 (0.21), residues: 1862 helix: -0.45 (0.21), residues: 504 sheet: 3.08 (0.20), residues: 602 loop : 0.32 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 526 HIS 0.004 0.001 HIS K 532 PHE 0.010 0.001 PHE A 444 TYR 0.011 0.002 TYR B 462 ARG 0.004 0.001 ARG C 410 Details of bonding type rmsd hydrogen bonds : bond 0.06497 ( 672) hydrogen bonds : angle 5.02406 ( 1764) covalent geometry : bond 0.00320 (15498) covalent geometry : angle 0.63765 (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 223 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 2.427 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: I 435 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7818 (mtpp) outliers start: 4 outliers final: 0 residues processed: 221 average time/residue: 2.3971 time to fit residues: 591.5946 Evaluate side-chains 194 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 101 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 ASN D 465 ASN J 465 ASN K 465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.181253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141717 restraints weight = 43525.459| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.19 r_work: 0.3348 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15498 Z= 0.164 Angle : 0.587 4.492 21042 Z= 0.320 Chirality : 0.043 0.123 2240 Planarity : 0.004 0.031 2800 Dihedral : 5.159 18.365 2044 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.87 % Allowed : 10.99 % Favored : 88.14 % 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: 1.30 (0.20), residues: 1862 helix: -0.20 (0.21), residues: 504 sheet: 2.73 (0.20), residues: 602 loop : 0.09 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 519 HIS 0.006 0.002 HIS J 530 PHE 0.016 0.002 PHE B 444 TYR 0.006 0.001 TYR L 462 ARG 0.002 0.000 ARG N 410 Details of bonding type rmsd hydrogen bonds : bond 0.05460 ( 672) hydrogen bonds : angle 4.40897 ( 1764) covalent geometry : bond 0.00379 (15498) covalent geometry : angle 0.58673 (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 206 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 2.368 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: I 435 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7874 (mtpp) outliers start: 14 outliers final: 14 residues processed: 194 average time/residue: 2.3522 time to fit residues: 510.8924 Evaluate side-chains 199 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain H residue 511 SER Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain J residue 511 SER Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain L residue 511 SER Chi-restraints excluded: chain N residue 511 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 122 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142808 restraints weight = 43603.521| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.20 r_work: 0.3324 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15498 Z= 0.138 Angle : 0.536 4.497 21042 Z= 0.287 Chirality : 0.042 0.122 2240 Planarity : 0.004 0.029 2800 Dihedral : 4.832 18.780 2044 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.81 % Allowed : 11.37 % Favored : 87.83 % 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: 1.62 (0.21), residues: 1862 helix: 0.29 (0.23), residues: 490 sheet: 2.18 (0.20), residues: 672 loop : 0.66 (0.27), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 519 HIS 0.005 0.001 HIS I 530 PHE 0.013 0.001 PHE I 444 TYR 0.006 0.001 TYR M 462 ARG 0.003 0.000 ARG M 521 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 672) hydrogen bonds : angle 4.15222 ( 1764) covalent geometry : bond 0.00320 (15498) covalent geometry : angle 0.53626 (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 227 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 2.689 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: G 456 MET cc_start: 0.7223 (mmm) cc_final: 0.6894 (mmm) REVERT: I 435 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7851 (mtpp) REVERT: N 456 MET cc_start: 0.7238 (mmm) cc_final: 0.6900 (mmm) outliers start: 13 outliers final: 9 residues processed: 218 average time/residue: 2.1906 time to fit residues: 539.1818 Evaluate side-chains 202 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain J residue 511 SER Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain N residue 511 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.180634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146717 restraints weight = 43899.672| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.93 r_work: 0.3335 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15498 Z= 0.184 Angle : 0.581 4.562 21042 Z= 0.315 Chirality : 0.043 0.128 2240 Planarity : 0.004 0.029 2800 Dihedral : 4.939 17.830 2044 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.06 % Allowed : 11.06 % Favored : 87.89 % 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: 1.31 (0.20), residues: 1862 helix: 0.13 (0.23), residues: 490 sheet: 2.30 (0.19), residues: 700 loop : -0.07 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 519 HIS 0.006 0.002 HIS F 484 PHE 0.015 0.002 PHE I 444 TYR 0.006 0.001 TYR F 462 ARG 0.002 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.05255 ( 672) hydrogen bonds : angle 4.23271 ( 1764) covalent geometry : bond 0.00444 (15498) covalent geometry : angle 0.58053 (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 225 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 2.808 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: G 456 MET cc_start: 0.7259 (mmm) cc_final: 0.6945 (mmm) REVERT: I 435 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7958 (mtpp) REVERT: N 435 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8110 (mttp) REVERT: N 456 MET cc_start: 0.7222 (mmm) cc_final: 0.6907 (mmm) outliers start: 17 outliers final: 17 residues processed: 213 average time/residue: 2.7323 time to fit residues: 660.0762 Evaluate side-chains 210 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain J residue 511 SER Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain L residue 431 GLU Chi-restraints excluded: chain L residue 511 SER Chi-restraints excluded: chain N residue 474 ILE Chi-restraints excluded: chain N residue 511 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 167 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.181156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149138 restraints weight = 43817.365| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.75 r_work: 0.3348 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15498 Z= 0.163 Angle : 0.550 4.464 21042 Z= 0.297 Chirality : 0.042 0.124 2240 Planarity : 0.004 0.032 2800 Dihedral : 4.869 18.001 2044 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.81 % Allowed : 12.05 % Favored : 87.14 % 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: 1.26 (0.20), residues: 1862 helix: 0.13 (0.23), residues: 490 sheet: 2.28 (0.19), residues: 700 loop : -0.15 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP N 519 HIS 0.005 0.002 HIS F 484 PHE 0.013 0.002 PHE B 444 TYR 0.006 0.001 TYR M 462 ARG 0.001 0.000 ARG C 410 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 672) hydrogen bonds : angle 4.19554 ( 1764) covalent geometry : bond 0.00386 (15498) covalent geometry : angle 0.55046 (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 222 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 2.582 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: G 435 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8122 (mttp) REVERT: G 456 MET cc_start: 0.7201 (mmm) cc_final: 0.6910 (mmm) REVERT: I 435 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7977 (mtpp) REVERT: N 435 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8130 (mttp) REVERT: N 456 MET cc_start: 0.7198 (mmm) cc_final: 0.6909 (mmm) outliers start: 13 outliers final: 11 residues processed: 215 average time/residue: 2.2059 time to fit residues: 538.1152 Evaluate side-chains 203 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain H residue 511 SER Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 511 SER Chi-restraints excluded: chain L residue 511 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 ASN K 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.183332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144368 restraints weight = 43517.290| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.18 r_work: 0.3323 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 15498 Z= 0.116 Angle : 0.501 4.332 21042 Z= 0.267 Chirality : 0.041 0.120 2240 Planarity : 0.004 0.035 2800 Dihedral : 4.625 18.255 2044 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.87 % Allowed : 11.80 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1862 helix: 0.42 (0.23), residues: 490 sheet: 2.17 (0.20), residues: 672 loop : 0.39 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 519 HIS 0.004 0.001 HIS D 484 PHE 0.011 0.001 PHE I 444 TYR 0.005 0.001 TYR F 462 ARG 0.002 0.000 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 672) hydrogen bonds : angle 4.03027 ( 1764) covalent geometry : bond 0.00268 (15498) covalent geometry : angle 0.50112 (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 221 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 2.419 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: G 435 LYS cc_start: 0.8231 (mtpp) cc_final: 0.8007 (mttp) REVERT: G 456 MET cc_start: 0.7088 (mmm) cc_final: 0.6826 (mmm) REVERT: I 435 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7854 (mtpp) REVERT: N 435 LYS cc_start: 0.8238 (mtpp) cc_final: 0.8013 (mttp) REVERT: N 456 MET cc_start: 0.7065 (mmm) cc_final: 0.6807 (mmm) outliers start: 14 outliers final: 11 residues processed: 212 average time/residue: 2.2797 time to fit residues: 543.1043 Evaluate side-chains 196 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain J residue 511 SER Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain L residue 511 SER Chi-restraints excluded: chain N residue 511 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 ASN K 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.182445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141310 restraints weight = 43594.162| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.03 r_work: 0.3293 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 15498 Z= 0.117 Angle : 0.504 5.026 21042 Z= 0.268 Chirality : 0.041 0.123 2240 Planarity : 0.004 0.034 2800 Dihedral : 4.542 17.911 2044 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.93 % Allowed : 12.24 % Favored : 86.83 % 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: 1.59 (0.21), residues: 1862 helix: 0.49 (0.24), residues: 490 sheet: 2.26 (0.20), residues: 672 loop : 0.34 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 519 HIS 0.005 0.001 HIS F 484 PHE 0.012 0.001 PHE B 444 TYR 0.005 0.001 TYR M 462 ARG 0.001 0.000 ARG I 410 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 672) hydrogen bonds : angle 3.98752 ( 1764) covalent geometry : bond 0.00274 (15498) covalent geometry : angle 0.50383 (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 220 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 2.373 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: G 435 LYS cc_start: 0.8243 (mtpp) cc_final: 0.8025 (mttp) REVERT: G 456 MET cc_start: 0.7108 (mmm) cc_final: 0.6853 (mmm) REVERT: I 435 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7924 (mttp) REVERT: N 435 LYS cc_start: 0.8235 (mtpp) cc_final: 0.8011 (mttp) REVERT: N 456 MET cc_start: 0.7101 (mmm) cc_final: 0.6845 (mmm) outliers start: 15 outliers final: 14 residues processed: 209 average time/residue: 2.2109 time to fit residues: 522.1016 Evaluate side-chains 204 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain H residue 511 SER Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain J residue 511 SER Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 511 SER Chi-restraints excluded: chain N residue 511 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 51 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 ASN K 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.183118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144497 restraints weight = 43689.946| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.15 r_work: 0.3372 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 15498 Z= 0.107 Angle : 0.487 4.278 21042 Z= 0.258 Chirality : 0.041 0.122 2240 Planarity : 0.004 0.034 2800 Dihedral : 4.464 18.094 2044 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.75 % Allowed : 12.36 % Favored : 86.89 % 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: 1.68 (0.21), residues: 1862 helix: 0.59 (0.24), residues: 490 sheet: 2.31 (0.20), residues: 672 loop : 0.38 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 519 HIS 0.004 0.001 HIS D 484 PHE 0.010 0.001 PHE B 444 TYR 0.005 0.001 TYR C 462 ARG 0.001 0.000 ARG I 410 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 672) hydrogen bonds : angle 3.92821 ( 1764) covalent geometry : bond 0.00250 (15498) covalent geometry : angle 0.48677 (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 215 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 2.381 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: G 435 LYS cc_start: 0.8246 (mtpp) cc_final: 0.8023 (mttp) REVERT: G 456 MET cc_start: 0.7046 (mmm) cc_final: 0.6808 (mmm) REVERT: I 435 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7908 (mttp) REVERT: N 435 LYS cc_start: 0.8235 (mtpp) cc_final: 0.8008 (mttp) REVERT: N 456 MET cc_start: 0.6977 (mmm) cc_final: 0.6750 (mmm) outliers start: 12 outliers final: 12 residues processed: 206 average time/residue: 2.2582 time to fit residues: 523.2404 Evaluate side-chains 211 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain H residue 511 SER Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain K residue 511 SER Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 511 SER Chi-restraints excluded: chain N residue 511 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 ASN K 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.181777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141781 restraints weight = 43836.080| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.88 r_work: 0.3336 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15498 Z= 0.151 Angle : 0.526 4.352 21042 Z= 0.282 Chirality : 0.042 0.125 2240 Planarity : 0.004 0.034 2800 Dihedral : 4.585 17.603 2044 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.50 % Allowed : 12.86 % Favored : 86.65 % 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: 1.53 (0.21), residues: 1862 helix: 0.44 (0.24), residues: 490 sheet: 2.27 (0.20), residues: 672 loop : 0.24 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 519 HIS 0.006 0.001 HIS D 484 PHE 0.013 0.002 PHE B 444 TYR 0.006 0.001 TYR M 462 ARG 0.001 0.000 ARG I 460 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 672) hydrogen bonds : angle 4.03821 ( 1764) covalent geometry : bond 0.00364 (15498) covalent geometry : angle 0.52562 (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 212 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 2.527 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: G 435 LYS cc_start: 0.8274 (mtpp) cc_final: 0.8047 (mttp) REVERT: G 456 MET cc_start: 0.7091 (mmm) cc_final: 0.6838 (mmm) REVERT: I 435 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7911 (mtpp) REVERT: N 435 LYS cc_start: 0.8268 (mtpp) cc_final: 0.8039 (mttp) REVERT: N 456 MET cc_start: 0.7086 (mmm) cc_final: 0.6834 (mmm) outliers start: 8 outliers final: 8 residues processed: 209 average time/residue: 2.4531 time to fit residues: 576.6295 Evaluate side-chains 202 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain I residue 511 SER Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain N residue 474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 ASN K 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.182235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143423 restraints weight = 43494.141| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.13 r_work: 0.3362 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15498 Z= 0.131 Angle : 0.514 6.236 21042 Z= 0.274 Chirality : 0.041 0.123 2240 Planarity : 0.004 0.034 2800 Dihedral : 4.570 17.860 2044 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.56 % Allowed : 12.98 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.21), residues: 1862 helix: 0.49 (0.24), residues: 490 sheet: 2.25 (0.20), residues: 672 loop : 0.29 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 519 HIS 0.005 0.001 HIS H 484 PHE 0.011 0.001 PHE B 444 TYR 0.006 0.001 TYR F 462 ARG 0.001 0.000 ARG E 509 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 672) hydrogen bonds : angle 4.00367 ( 1764) covalent geometry : bond 0.00310 (15498) covalent geometry : angle 0.51370 (21042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18283.29 seconds wall clock time: 316 minutes 36.52 seconds (18996.52 seconds total)