Starting phenix.real_space_refine on Wed Aug 27 02:10:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8orb_17119/08_2025/8orb_17119_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8orb_17119/08_2025/8orb_17119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8orb_17119/08_2025/8orb_17119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8orb_17119/08_2025/8orb_17119.map" model { file = "/net/cci-nas-00/data/ceres_data/8orb_17119/08_2025/8orb_17119_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8orb_17119/08_2025/8orb_17119_neut.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 sd= 0.157 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: 4 Type Number sf(0) Gaussians S 240 5.16 5 C 29376 2.51 5 N 7992 2.21 5 O 8376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45984 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y Time building chain proxies: 3.86, per 1000 atoms: 0.08 Number of scatterers: 45984 At special positions: 0 Unit cell: (147.65, 147.65, 147.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 240 16.00 O 8376 8.00 N 7992 7.00 C 29376 6.00 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: 3.21 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 476.8 nanoseconds 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10944 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 120 sheets defined 43.7% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'A' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS A 516 " --> pdb=" O VAL A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 517 through 534 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL A 628 " --> pdb=" O ARG A 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 396 Processing helix chain 'B' and resid 405 through 422 Processing helix chain 'B' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS B 516 " --> pdb=" O VAL B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 516' Processing helix chain 'B' and resid 517 through 534 Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 405 through 422 Processing helix chain 'C' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 450 " --> pdb=" O GLU C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE C 461 " --> pdb=" O THR C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS C 516 " --> pdb=" O VAL C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 516' Processing helix chain 'C' and resid 517 through 534 Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL C 628 " --> pdb=" O ARG C 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 396 Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 450 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE D 461 " --> pdb=" O THR D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS D 516 " --> pdb=" O VAL D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 516' Processing helix chain 'D' and resid 517 through 534 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E 450 " --> pdb=" O GLU E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS E 516 " --> pdb=" O VAL E 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 513 through 516' Processing helix chain 'E' and resid 517 through 534 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 606 through 623 Processing helix chain 'E' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG F 450 " --> pdb=" O GLU F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE F 461 " --> pdb=" O THR F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS F 516 " --> pdb=" O VAL F 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 513 through 516' Processing helix chain 'F' and resid 517 through 534 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 606 through 623 Processing helix chain 'F' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL F 628 " --> pdb=" O ARG F 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 396 Processing helix chain 'G' and resid 405 through 422 Processing helix chain 'G' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG G 450 " --> pdb=" O GLU G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE G 461 " --> pdb=" O THR G 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS G 516 " --> pdb=" O VAL G 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 513 through 516' Processing helix chain 'G' and resid 517 through 534 Processing helix chain 'G' and resid 538 through 542 Processing helix chain 'G' and resid 606 through 623 Processing helix chain 'G' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL G 628 " --> pdb=" O ARG G 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 396 Processing helix chain 'H' and resid 405 through 422 Processing helix chain 'H' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS H 449 " --> pdb=" O GLU H 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 450 " --> pdb=" O GLU H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE H 461 " --> pdb=" O THR H 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS H 516 " --> pdb=" O VAL H 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 513 through 516' Processing helix chain 'H' and resid 517 through 534 Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 606 through 623 Processing helix chain 'H' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL H 628 " --> pdb=" O ARG H 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 396 Processing helix chain 'I' and resid 405 through 422 Processing helix chain 'I' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS I 449 " --> pdb=" O GLU I 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG I 450 " --> pdb=" O GLU I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE I 461 " --> pdb=" O THR I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS I 516 " --> pdb=" O VAL I 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 513 through 516' Processing helix chain 'I' and resid 517 through 534 Processing helix chain 'I' and resid 538 through 542 Processing helix chain 'I' and resid 606 through 623 Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL I 628 " --> pdb=" O ARG I 625 " (cutoff:3.500A) Processing helix chain 'J' and resid 392 through 396 Processing helix chain 'J' and resid 405 through 422 Processing helix chain 'J' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS J 449 " --> pdb=" O GLU J 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG J 450 " --> pdb=" O GLU J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE J 461 " --> pdb=" O THR J 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS J 516 " --> pdb=" O VAL J 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 513 through 516' Processing helix chain 'J' and resid 517 through 534 Processing helix chain 'J' and resid 538 through 542 Processing helix chain 'J' and resid 606 through 623 Processing helix chain 'J' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL J 628 " --> pdb=" O ARG J 625 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 396 Processing helix chain 'K' and resid 405 through 422 Processing helix chain 'K' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS K 449 " --> pdb=" O GLU K 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG K 450 " --> pdb=" O GLU K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE K 461 " --> pdb=" O THR K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS K 516 " --> pdb=" O VAL K 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 513 through 516' Processing helix chain 'K' and resid 517 through 534 Processing helix chain 'K' and resid 538 through 542 Processing helix chain 'K' and resid 606 through 623 Processing helix chain 'K' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL K 628 " --> pdb=" O ARG K 625 " (cutoff:3.500A) Processing helix chain 'L' and resid 392 through 396 Processing helix chain 'L' and resid 405 through 422 Processing helix chain 'L' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS L 449 " --> pdb=" O GLU L 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG L 450 " --> pdb=" O GLU L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE L 461 " --> pdb=" O THR L 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS L 516 " --> pdb=" O VAL L 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 513 through 516' Processing helix chain 'L' and resid 517 through 534 Processing helix chain 'L' and resid 538 through 542 Processing helix chain 'L' and resid 606 through 623 Processing helix chain 'L' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL L 628 " --> pdb=" O ARG L 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 396 Processing helix chain 'M' and resid 405 through 422 Processing helix chain 'M' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS M 449 " --> pdb=" O GLU M 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG M 450 " --> pdb=" O GLU M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE M 461 " --> pdb=" O THR M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS M 516 " --> pdb=" O VAL M 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 513 through 516' Processing helix chain 'M' and resid 517 through 534 Processing helix chain 'M' and resid 538 through 542 Processing helix chain 'M' and resid 606 through 623 Processing helix chain 'M' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL M 628 " --> pdb=" O ARG M 625 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 396 Processing helix chain 'N' and resid 405 through 422 Processing helix chain 'N' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS N 449 " --> pdb=" O GLU N 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG N 450 " --> pdb=" O GLU N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE N 461 " --> pdb=" O THR N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS N 516 " --> pdb=" O VAL N 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 513 through 516' Processing helix chain 'N' and resid 517 through 534 Processing helix chain 'N' and resid 538 through 542 Processing helix chain 'N' and resid 606 through 623 Processing helix chain 'N' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL N 628 " --> pdb=" O ARG N 625 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 396 Processing helix chain 'O' and resid 405 through 422 Processing helix chain 'O' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS O 449 " --> pdb=" O GLU O 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG O 450 " --> pdb=" O GLU O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE O 461 " --> pdb=" O THR O 457 " (cutoff:3.500A) Processing helix chain 'O' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS O 516 " --> pdb=" O VAL O 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 513 through 516' Processing helix chain 'O' and resid 517 through 534 Processing helix chain 'O' and resid 538 through 542 Processing helix chain 'O' and resid 606 through 623 Processing helix chain 'O' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL O 628 " --> pdb=" O ARG O 625 " (cutoff:3.500A) Processing helix chain 'P' and resid 392 through 396 Processing helix chain 'P' and resid 405 through 422 Processing helix chain 'P' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS P 449 " --> pdb=" O GLU P 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG P 450 " --> pdb=" O GLU P 446 " (cutoff:3.500A) Processing helix chain 'P' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE P 461 " --> pdb=" O THR P 457 " (cutoff:3.500A) Processing helix chain 'P' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS P 516 " --> pdb=" O VAL P 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 513 through 516' Processing helix chain 'P' and resid 517 through 534 Processing helix chain 'P' and resid 538 through 542 Processing helix chain 'P' and resid 606 through 623 Processing helix chain 'P' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL P 628 " --> pdb=" O ARG P 625 " (cutoff:3.500A) Processing helix chain 'Q' and resid 392 through 396 Processing helix chain 'Q' and resid 405 through 422 Processing helix chain 'Q' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS Q 449 " --> pdb=" O GLU Q 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG Q 450 " --> pdb=" O GLU Q 446 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE Q 461 " --> pdb=" O THR Q 457 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS Q 516 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 513 through 516' Processing helix chain 'Q' and resid 517 through 534 Processing helix chain 'Q' and resid 538 through 542 Processing helix chain 'Q' and resid 606 through 623 Processing helix chain 'Q' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL Q 628 " --> pdb=" O ARG Q 625 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 396 Processing helix chain 'R' and resid 405 through 422 Processing helix chain 'R' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS R 449 " --> pdb=" O GLU R 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG R 450 " --> pdb=" O GLU R 446 " (cutoff:3.500A) Processing helix chain 'R' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE R 461 " --> pdb=" O THR R 457 " (cutoff:3.500A) Processing helix chain 'R' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS R 516 " --> pdb=" O VAL R 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 513 through 516' Processing helix chain 'R' and resid 517 through 534 Processing helix chain 'R' and resid 538 through 542 Processing helix chain 'R' and resid 606 through 623 Processing helix chain 'R' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL R 628 " --> pdb=" O ARG R 625 " (cutoff:3.500A) Processing helix chain 'S' and resid 392 through 396 Processing helix chain 'S' and resid 405 through 422 Processing helix chain 'S' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS S 449 " --> pdb=" O GLU S 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG S 450 " --> pdb=" O GLU S 446 " (cutoff:3.500A) Processing helix chain 'S' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE S 461 " --> pdb=" O THR S 457 " (cutoff:3.500A) Processing helix chain 'S' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS S 516 " --> pdb=" O VAL S 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 513 through 516' Processing helix chain 'S' and resid 517 through 534 Processing helix chain 'S' and resid 538 through 542 Processing helix chain 'S' and resid 606 through 623 Processing helix chain 'S' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL S 628 " --> pdb=" O ARG S 625 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 396 Processing helix chain 'T' and resid 405 through 422 Processing helix chain 'T' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS T 449 " --> pdb=" O GLU T 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG T 450 " --> pdb=" O GLU T 446 " (cutoff:3.500A) Processing helix chain 'T' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE T 461 " --> pdb=" O THR T 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS T 516 " --> pdb=" O VAL T 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 513 through 516' Processing helix chain 'T' and resid 517 through 534 Processing helix chain 'T' and resid 538 through 542 Processing helix chain 'T' and resid 606 through 623 Processing helix chain 'T' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL T 628 " --> pdb=" O ARG T 625 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 396 Processing helix chain 'V' and resid 405 through 422 Processing helix chain 'V' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS V 449 " --> pdb=" O GLU V 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG V 450 " --> pdb=" O GLU V 446 " (cutoff:3.500A) Processing helix chain 'V' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE V 461 " --> pdb=" O THR V 457 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS V 516 " --> pdb=" O VAL V 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 513 through 516' Processing helix chain 'V' and resid 517 through 534 Processing helix chain 'V' and resid 538 through 542 Processing helix chain 'V' and resid 606 through 623 Processing helix chain 'V' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL V 628 " --> pdb=" O ARG V 625 " (cutoff:3.500A) Processing helix chain 'W' and resid 392 through 396 Processing helix chain 'W' and resid 405 through 422 Processing helix chain 'W' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS W 449 " --> pdb=" O GLU W 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG W 450 " --> pdb=" O GLU W 446 " (cutoff:3.500A) Processing helix chain 'W' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE W 461 " --> pdb=" O THR W 457 " (cutoff:3.500A) Processing helix chain 'W' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS W 516 " --> pdb=" O VAL W 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 513 through 516' Processing helix chain 'W' and resid 517 through 534 Processing helix chain 'W' and resid 538 through 542 Processing helix chain 'W' and resid 606 through 623 Processing helix chain 'W' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL W 628 " --> pdb=" O ARG W 625 " (cutoff:3.500A) Processing helix chain 'X' and resid 392 through 396 Processing helix chain 'X' and resid 405 through 422 Processing helix chain 'X' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS X 449 " --> pdb=" O GLU X 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG X 450 " --> pdb=" O GLU X 446 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE X 461 " --> pdb=" O THR X 457 " (cutoff:3.500A) Processing helix chain 'X' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS X 516 " --> pdb=" O VAL X 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 513 through 516' Processing helix chain 'X' and resid 517 through 534 Processing helix chain 'X' and resid 538 through 542 Processing helix chain 'X' and resid 606 through 623 Processing helix chain 'X' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL X 628 " --> pdb=" O ARG X 625 " (cutoff:3.500A) Processing helix chain 'Y' and resid 392 through 396 Processing helix chain 'Y' and resid 405 through 422 Processing helix chain 'Y' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS Y 449 " --> pdb=" O GLU Y 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG Y 450 " --> pdb=" O GLU Y 446 " (cutoff:3.500A) Processing helix chain 'Y' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE Y 461 " --> pdb=" O THR Y 457 " (cutoff:3.500A) Processing helix chain 'Y' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS Y 516 " --> pdb=" O VAL Y 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 513 through 516' Processing helix chain 'Y' and resid 517 through 534 Processing helix chain 'Y' and resid 538 through 542 Processing helix chain 'Y' and resid 606 through 623 Processing helix chain 'Y' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL Y 628 " --> pdb=" O ARG Y 625 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR A 548 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL A 574 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 550 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR A 548 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL A 574 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 550 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 478 through 480 Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 501 Processing sheet with id=AA7, first strand: chain 'A' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR G 548 " --> pdb=" O LEU G 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL G 574 " --> pdb=" O THR G 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER G 550 " --> pdb=" O VAL G 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AA9, first strand: chain 'B' and resid 399 through 403 Processing sheet with id=AB1, first strand: chain 'B' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR B 548 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL B 574 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER B 550 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR B 548 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL B 574 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER B 550 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 478 through 480 Processing sheet with id=AB4, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AB5, first strand: chain 'B' and resid 499 through 501 Processing sheet with id=AB6, first strand: chain 'B' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR M 548 " --> pdb=" O LEU M 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL M 574 " --> pdb=" O THR M 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER M 550 " --> pdb=" O VAL M 574 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 559 through 560 Processing sheet with id=AB8, first strand: chain 'C' and resid 399 through 403 Processing sheet with id=AB9, first strand: chain 'C' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR C 548 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 574 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER C 550 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR C 548 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 574 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER C 550 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 478 through 480 Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AC4, first strand: chain 'C' and resid 499 through 501 Processing sheet with id=AC5, first strand: chain 'C' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR P 548 " --> pdb=" O LEU P 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL P 574 " --> pdb=" O THR P 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER P 550 " --> pdb=" O VAL P 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 559 through 560 Processing sheet with id=AC7, first strand: chain 'D' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR D 548 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL D 574 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER D 550 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR D 548 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL D 574 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER D 550 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 478 through 480 Processing sheet with id=AD1, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AD2, first strand: chain 'D' and resid 499 through 501 Processing sheet with id=AD3, first strand: chain 'E' and resid 399 through 403 Processing sheet with id=AD4, first strand: chain 'E' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR E 548 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 574 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER E 550 " --> pdb=" O VAL E 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR E 548 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 574 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER E 550 " --> pdb=" O VAL E 574 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 478 through 480 Processing sheet with id=AD7, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AD8, first strand: chain 'E' and resid 499 through 501 Processing sheet with id=AD9, first strand: chain 'E' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR W 548 " --> pdb=" O LEU W 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL W 574 " --> pdb=" O THR W 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER W 550 " --> pdb=" O VAL W 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 559 through 560 Processing sheet with id=AE2, first strand: chain 'F' and resid 399 through 403 Processing sheet with id=AE3, first strand: chain 'F' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR F 548 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL F 574 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER F 550 " --> pdb=" O VAL F 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR F 548 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL F 574 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER F 550 " --> pdb=" O VAL F 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 478 through 480 Processing sheet with id=AE6, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AE7, first strand: chain 'F' and resid 499 through 501 Processing sheet with id=AE8, first strand: chain 'F' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR H 548 " --> pdb=" O LEU H 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL H 574 " --> pdb=" O THR H 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER H 550 " --> pdb=" O VAL H 574 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 559 through 560 Processing sheet with id=AF1, first strand: chain 'G' and resid 494 through 496 Processing sheet with id=AF2, first strand: chain 'G' and resid 499 through 501 Processing sheet with id=AF3, first strand: chain 'H' and resid 399 through 403 Processing sheet with id=AF4, first strand: chain 'H' and resid 494 through 496 Processing sheet with id=AF5, first strand: chain 'H' and resid 499 through 501 Processing sheet with id=AF6, first strand: chain 'H' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR X 548 " --> pdb=" O LEU X 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL X 574 " --> pdb=" O THR X 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER X 550 " --> pdb=" O VAL X 574 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 559 through 560 Processing sheet with id=AF8, first strand: chain 'I' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR I 548 " --> pdb=" O LEU I 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL I 574 " --> pdb=" O THR I 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER I 550 " --> pdb=" O VAL I 574 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR I 548 " --> pdb=" O LEU I 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL I 574 " --> pdb=" O THR I 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER I 550 " --> pdb=" O VAL I 574 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 478 through 480 Processing sheet with id=AG2, first strand: chain 'I' and resid 494 through 496 Processing sheet with id=AG3, first strand: chain 'I' and resid 499 through 501 Processing sheet with id=AG4, first strand: chain 'J' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR J 548 " --> pdb=" O LEU J 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL J 574 " --> pdb=" O THR J 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER J 550 " --> pdb=" O VAL J 574 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR J 548 " --> pdb=" O LEU J 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL J 574 " --> pdb=" O THR J 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER J 550 " --> pdb=" O VAL J 574 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 478 through 480 Processing sheet with id=AG7, first strand: chain 'J' and resid 494 through 496 Processing sheet with id=AG8, first strand: chain 'J' and resid 499 through 501 Processing sheet with id=AG9, first strand: chain 'K' and resid 399 through 403 Processing sheet with id=AH1, first strand: chain 'K' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR K 548 " --> pdb=" O LEU K 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL K 574 " --> pdb=" O THR K 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER K 550 " --> pdb=" O VAL K 574 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR K 548 " --> pdb=" O LEU K 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL K 574 " --> pdb=" O THR K 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER K 550 " --> pdb=" O VAL K 574 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 478 through 480 Processing sheet with id=AH4, first strand: chain 'K' and resid 494 through 496 Processing sheet with id=AH5, first strand: chain 'K' and resid 499 through 501 Processing sheet with id=AH6, first strand: chain 'K' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR Q 548 " --> pdb=" O LEU Q 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL Q 574 " --> pdb=" O THR Q 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER Q 550 " --> pdb=" O VAL Q 574 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 559 through 560 Processing sheet with id=AH8, first strand: chain 'L' and resid 399 through 403 Processing sheet with id=AH9, first strand: chain 'L' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR L 548 " --> pdb=" O LEU L 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL L 574 " --> pdb=" O THR L 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER L 550 " --> pdb=" O VAL L 574 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR L 548 " --> pdb=" O LEU L 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL L 574 " --> pdb=" O THR L 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER L 550 " --> pdb=" O VAL L 574 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 478 through 480 Processing sheet with id=AI3, first strand: chain 'L' and resid 494 through 496 Processing sheet with id=AI4, first strand: chain 'L' and resid 499 through 501 Processing sheet with id=AI5, first strand: chain 'L' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR N 548 " --> pdb=" O LEU N 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL N 574 " --> pdb=" O THR N 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER N 550 " --> pdb=" O VAL N 574 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 559 through 560 Processing sheet with id=AI7, first strand: chain 'M' and resid 494 through 496 Processing sheet with id=AI8, first strand: chain 'M' and resid 499 through 501 Processing sheet with id=AI9, first strand: chain 'N' and resid 399 through 403 Processing sheet with id=AJ1, first strand: chain 'N' and resid 494 through 496 Processing sheet with id=AJ2, first strand: chain 'N' and resid 499 through 501 Processing sheet with id=AJ3, first strand: chain 'N' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR R 548 " --> pdb=" O LEU R 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL R 574 " --> pdb=" O THR R 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER R 550 " --> pdb=" O VAL R 574 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 559 through 560 Processing sheet with id=AJ5, first strand: chain 'O' and resid 399 through 403 Processing sheet with id=AJ6, first strand: chain 'O' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR O 548 " --> pdb=" O LEU O 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL O 574 " --> pdb=" O THR O 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER O 550 " --> pdb=" O VAL O 574 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR O 548 " --> pdb=" O LEU O 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL O 574 " --> pdb=" O THR O 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER O 550 " --> pdb=" O VAL O 574 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 478 through 480 Processing sheet with id=AJ9, first strand: chain 'O' and resid 494 through 496 Processing sheet with id=AK1, first strand: chain 'O' and resid 499 through 501 Processing sheet with id=AK2, first strand: chain 'O' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR T 548 " --> pdb=" O LEU T 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL T 574 " --> pdb=" O THR T 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER T 550 " --> pdb=" O VAL T 574 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 559 through 560 Processing sheet with id=AK4, first strand: chain 'P' and resid 494 through 496 Processing sheet with id=AK5, first strand: chain 'P' and resid 499 through 501 Processing sheet with id=AK6, first strand: chain 'Q' and resid 399 through 403 Processing sheet with id=AK7, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id=AK8, first strand: chain 'Q' and resid 499 through 501 Processing sheet with id=AK9, first strand: chain 'Q' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR V 548 " --> pdb=" O LEU V 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL V 574 " --> pdb=" O THR V 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER V 550 " --> pdb=" O VAL V 574 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Q' and resid 559 through 560 Processing sheet with id=AL2, first strand: chain 'R' and resid 494 through 496 Processing sheet with id=AL3, first strand: chain 'R' and resid 499 through 501 Processing sheet with id=AL4, first strand: chain 'S' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR S 548 " --> pdb=" O LEU S 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL S 574 " --> pdb=" O THR S 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER S 550 " --> pdb=" O VAL S 574 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'S' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR S 548 " --> pdb=" O LEU S 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL S 574 " --> pdb=" O THR S 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER S 550 " --> pdb=" O VAL S 574 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'S' and resid 478 through 480 Processing sheet with id=AL7, first strand: chain 'S' and resid 494 through 496 Processing sheet with id=AL8, first strand: chain 'S' and resid 499 through 501 Processing sheet with id=AL9, first strand: chain 'T' and resid 399 through 403 Processing sheet with id=AM1, first strand: chain 'T' and resid 494 through 496 Processing sheet with id=AM2, first strand: chain 'T' and resid 499 through 501 Processing sheet with id=AM3, first strand: chain 'T' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR Y 548 " --> pdb=" O LEU Y 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL Y 574 " --> pdb=" O THR Y 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER Y 550 " --> pdb=" O VAL Y 574 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'T' and resid 559 through 560 Processing sheet with id=AM5, first strand: chain 'V' and resid 494 through 496 Processing sheet with id=AM6, first strand: chain 'V' and resid 499 through 501 Processing sheet with id=AM7, first strand: chain 'W' and resid 494 through 496 Processing sheet with id=AM8, first strand: chain 'W' and resid 499 through 501 Processing sheet with id=AM9, first strand: chain 'X' and resid 494 through 496 Processing sheet with id=AN1, first strand: chain 'X' and resid 499 through 501 Processing sheet with id=AN2, first strand: chain 'Y' and resid 494 through 496 Processing sheet with id=AN3, first strand: chain 'Y' and resid 499 through 501 2568 hydrogen bonds defined for protein. 6912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.21 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15096 1.34 - 1.46: 8196 1.46 - 1.58: 23076 1.58 - 1.69: 0 1.69 - 1.81: 456 Bond restraints: 46824 Sorted by residual: bond pdb=" CA PHE W 547 " pdb=" C PHE W 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 bond pdb=" CA PHE O 547 " pdb=" C PHE O 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 bond pdb=" CA PHE S 547 " pdb=" C PHE S 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 bond pdb=" CA PHE G 547 " pdb=" C PHE G 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 bond pdb=" CA PHE K 547 " pdb=" C PHE K 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 ... (remaining 46819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 59724 0.78 - 1.57: 2796 1.57 - 2.35: 408 2.35 - 3.13: 216 3.13 - 3.92: 48 Bond angle restraints: 63192 Sorted by residual: angle pdb=" NE ARG L 625 " pdb=" CZ ARG L 625 " pdb=" NH2 ARG L 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 angle pdb=" NE ARG S 625 " pdb=" CZ ARG S 625 " pdb=" NH2 ARG S 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 angle pdb=" NE ARG E 625 " pdb=" CZ ARG E 625 " pdb=" NH2 ARG E 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 angle pdb=" NE ARG A 625 " pdb=" CZ ARG A 625 " pdb=" NH2 ARG A 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 angle pdb=" NE ARG K 625 " pdb=" CZ ARG K 625 " pdb=" NH2 ARG K 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 ... (remaining 63187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.28: 27096 11.28 - 22.56: 1224 22.56 - 33.83: 216 33.83 - 45.11: 72 45.11 - 56.39: 96 Dihedral angle restraints: 28704 sinusoidal: 11832 harmonic: 16872 Sorted by residual: dihedral pdb=" CA LYS B 455 " pdb=" CB LYS B 455 " pdb=" CG LYS B 455 " pdb=" CD LYS B 455 " ideal model delta sinusoidal sigma weight residual -180.00 -123.61 -56.39 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA LYS N 455 " pdb=" CB LYS N 455 " pdb=" CG LYS N 455 " pdb=" CD LYS N 455 " ideal model delta sinusoidal sigma weight residual -180.00 -123.61 -56.39 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA LYS I 455 " pdb=" CB LYS I 455 " pdb=" CG LYS I 455 " pdb=" CD LYS I 455 " ideal model delta sinusoidal sigma weight residual -180.00 -123.61 -56.39 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 28701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 4272 0.025 - 0.050: 1872 0.050 - 0.075: 480 0.075 - 0.100: 432 0.100 - 0.125: 240 Chirality restraints: 7296 Sorted by residual: chirality pdb=" CA VAL V 425 " pdb=" N VAL V 425 " pdb=" C VAL V 425 " pdb=" CB VAL V 425 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL I 425 " pdb=" N VAL I 425 " pdb=" C VAL I 425 " pdb=" CB VAL I 425 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL T 425 " pdb=" N VAL T 425 " pdb=" C VAL T 425 " pdb=" CB VAL T 425 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 7293 not shown) Planarity restraints: 8064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 501 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO N 502 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO N 502 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO N 502 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 501 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO M 502 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO M 502 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO M 502 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 501 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO G 502 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO G 502 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 502 " 0.015 5.00e-02 4.00e+02 ... (remaining 8061 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 14304 2.84 - 3.35: 41820 3.35 - 3.87: 76440 3.87 - 4.38: 87240 4.38 - 4.90: 152268 Nonbonded interactions: 372072 Sorted by model distance: nonbonded pdb=" O GLY B 556 " pdb=" OG1 THR B 557 " model vdw 2.322 3.040 nonbonded pdb=" O GLY Q 556 " pdb=" OG1 THR Q 557 " model vdw 2.322 3.040 nonbonded pdb=" O GLY L 556 " pdb=" OG1 THR L 557 " model vdw 2.322 3.040 nonbonded pdb=" O GLY A 556 " pdb=" OG1 THR A 557 " model vdw 2.322 3.040 nonbonded pdb=" O GLY O 556 " pdb=" OG1 THR O 557 " model vdw 2.322 3.040 ... (remaining 372067 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 1.260 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.970 Find NCS groups from input model: 0.350 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.002 0.017 46824 Z= 0.101 Angle : 0.416 3.915 63192 Z= 0.251 Chirality : 0.039 0.125 7296 Planarity : 0.004 0.028 8064 Dihedral : 7.781 56.389 17760 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.47 % Allowed : 3.79 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.12), residues: 5880 helix: 2.88 (0.11), residues: 2088 sheet: 0.03 (0.15), residues: 1392 loop : -0.04 (0.14), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 417 TYR 0.001 0.000 TYR P 492 PHE 0.009 0.001 PHE A 613 TRP 0.004 0.001 TRP Q 583 HIS 0.001 0.001 HIS S 559 Details of bonding type rmsd covalent geometry : bond 0.00163 (46824) covalent geometry : angle 0.41621 (63192) hydrogen bonds : bond 0.14885 ( 2424) hydrogen bonds : angle 5.32153 ( 6912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 870 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 593 MET cc_start: 0.8292 (mmm) cc_final: 0.8074 (mmm) REVERT: D 385 MET cc_start: 0.4596 (ptt) cc_final: 0.4299 (mmm) REVERT: H 593 MET cc_start: 0.8314 (mmm) cc_final: 0.8064 (mmm) REVERT: I 385 MET cc_start: 0.4546 (ptt) cc_final: 0.4311 (mmm) REVERT: J 385 MET cc_start: 0.4593 (ptt) cc_final: 0.4311 (mmm) REVERT: J 593 MET cc_start: 0.8314 (mmm) cc_final: 0.8064 (mmm) REVERT: K 593 MET cc_start: 0.8314 (mmm) cc_final: 0.8064 (mmm) REVERT: L 593 MET cc_start: 0.8292 (mmm) cc_final: 0.8069 (mmm) REVERT: M 385 MET cc_start: 0.4563 (ptt) cc_final: 0.4324 (mmm) REVERT: O 593 MET cc_start: 0.8292 (mmm) cc_final: 0.8074 (mmm) REVERT: P 385 MET cc_start: 0.4551 (ptt) cc_final: 0.4319 (mmm) REVERT: R 385 MET cc_start: 0.4603 (ptt) cc_final: 0.4312 (mmm) REVERT: S 385 MET cc_start: 0.4633 (ptt) cc_final: 0.4313 (mmm) REVERT: V 385 MET cc_start: 0.4567 (ptt) cc_final: 0.4333 (mmm) REVERT: W 385 MET cc_start: 0.4636 (ptt) cc_final: 0.4317 (mmm) REVERT: X 385 MET cc_start: 0.4571 (ptt) cc_final: 0.4304 (mmm) REVERT: Y 385 MET cc_start: 0.4600 (ptt) cc_final: 0.4307 (mmm) outliers start: 24 outliers final: 0 residues processed: 894 average time/residue: 0.2748 time to fit residues: 387.5705 Evaluate side-chains 567 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 0.3980 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN A 444 ASN ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN B 444 ASN ** C 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN C 444 ASN ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN D 444 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN E 444 ASN ** F 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN F 444 ASN ** G 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN G 444 ASN ** H 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN H 444 ASN ** I 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN I 444 ASN ** J 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN J 444 ASN ** K 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN K 444 ASN ** L 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 443 GLN L 444 ASN ** M 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 443 GLN M 444 ASN ** N 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 443 GLN N 444 ASN ** O 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 444 ASN ** P 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 443 GLN P 444 ASN ** Q 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 443 GLN Q 444 ASN ** R 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 443 GLN R 444 ASN ** S 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 443 GLN S 444 ASN ** T 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 443 GLN T 444 ASN ** V 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 GLN V 444 ASN ** W 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 443 GLN W 444 ASN ** X 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 443 GLN X 444 ASN ** Y 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 GLN Y 444 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.222523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.184323 restraints weight = 47047.113| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.85 r_work: 0.3821 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 46824 Z= 0.181 Angle : 0.533 5.914 63192 Z= 0.287 Chirality : 0.045 0.126 7296 Planarity : 0.005 0.033 8064 Dihedral : 3.568 12.583 6240 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.48 % Favored : 98.11 % Rotamer: Outliers : 0.77 % Allowed : 6.71 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.11), residues: 5880 helix: 2.57 (0.11), residues: 2136 sheet: 0.15 (0.15), residues: 1152 loop : -0.08 (0.13), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 450 TYR 0.003 0.001 TYR G 492 PHE 0.014 0.002 PHE D 547 TRP 0.010 0.002 TRP A 583 HIS 0.006 0.002 HIS G 559 Details of bonding type rmsd covalent geometry : bond 0.00444 (46824) covalent geometry : angle 0.53331 (63192) hydrogen bonds : bond 0.04196 ( 2424) hydrogen bonds : angle 4.49745 ( 6912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 600 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.7393 (t0) cc_final: 0.7112 (t0) REVERT: A 536 LYS cc_start: 0.8742 (mttt) cc_final: 0.8339 (mttp) REVERT: B 534 ASP cc_start: 0.7395 (t0) cc_final: 0.7146 (t0) REVERT: B 536 LYS cc_start: 0.8746 (mttt) cc_final: 0.8373 (mttp) REVERT: C 534 ASP cc_start: 0.7361 (t0) cc_final: 0.6364 (t0) REVERT: C 536 LYS cc_start: 0.8711 (mttt) cc_final: 0.8225 (mttm) REVERT: E 534 ASP cc_start: 0.7424 (t0) cc_final: 0.7077 (t0) REVERT: E 536 LYS cc_start: 0.8743 (mttt) cc_final: 0.8334 (mttp) REVERT: G 534 ASP cc_start: 0.7399 (t0) cc_final: 0.7053 (t0) REVERT: G 536 LYS cc_start: 0.8729 (mttt) cc_final: 0.8318 (mttp) REVERT: H 453 ASP cc_start: 0.7580 (t70) cc_final: 0.7037 (t0) REVERT: H 534 ASP cc_start: 0.7461 (t0) cc_final: 0.7023 (t0) REVERT: H 536 LYS cc_start: 0.8713 (mttt) cc_final: 0.8310 (mttp) REVERT: I 385 MET cc_start: 0.4793 (ptt) cc_final: 0.4543 (mmm) REVERT: I 534 ASP cc_start: 0.7344 (t0) cc_final: 0.6357 (t0) REVERT: I 536 LYS cc_start: 0.8713 (mttt) cc_final: 0.8227 (mttm) REVERT: J 453 ASP cc_start: 0.7606 (t70) cc_final: 0.7059 (t0) REVERT: J 534 ASP cc_start: 0.7456 (t0) cc_final: 0.6460 (t0) REVERT: J 536 LYS cc_start: 0.8714 (mttt) cc_final: 0.8241 (mttm) REVERT: K 453 ASP cc_start: 0.7585 (t70) cc_final: 0.7037 (t0) REVERT: K 534 ASP cc_start: 0.7450 (t0) cc_final: 0.7007 (t0) REVERT: K 536 LYS cc_start: 0.8722 (mttt) cc_final: 0.8314 (mttp) REVERT: L 453 ASP cc_start: 0.7580 (t70) cc_final: 0.7022 (t0) REVERT: L 534 ASP cc_start: 0.7374 (t0) cc_final: 0.7099 (t0) REVERT: L 536 LYS cc_start: 0.8736 (mttt) cc_final: 0.8329 (mttp) REVERT: N 534 ASP cc_start: 0.7397 (t0) cc_final: 0.7048 (t0) REVERT: N 536 LYS cc_start: 0.8723 (mttt) cc_final: 0.8311 (mttp) REVERT: O 534 ASP cc_start: 0.7381 (t0) cc_final: 0.7110 (t0) REVERT: O 536 LYS cc_start: 0.8738 (mttt) cc_final: 0.8339 (mttp) REVERT: P 385 MET cc_start: 0.4794 (ptt) cc_final: 0.4569 (mmm) REVERT: P 534 ASP cc_start: 0.7365 (t0) cc_final: 0.6378 (t0) REVERT: P 536 LYS cc_start: 0.8718 (mttt) cc_final: 0.8234 (mttm) REVERT: Q 534 ASP cc_start: 0.7413 (t0) cc_final: 0.7156 (t0) REVERT: Q 536 LYS cc_start: 0.8743 (mttt) cc_final: 0.8371 (mttp) REVERT: S 534 ASP cc_start: 0.7418 (t0) cc_final: 0.7071 (t0) REVERT: S 536 LYS cc_start: 0.8731 (mttt) cc_final: 0.8319 (mttp) REVERT: T 534 ASP cc_start: 0.7393 (t0) cc_final: 0.7143 (t0) REVERT: T 536 LYS cc_start: 0.8720 (mttt) cc_final: 0.8344 (mttp) REVERT: W 534 ASP cc_start: 0.7437 (t0) cc_final: 0.7084 (t0) REVERT: W 536 LYS cc_start: 0.8736 (mttt) cc_final: 0.8327 (mttp) REVERT: X 534 ASP cc_start: 0.7383 (t0) cc_final: 0.7025 (t0) REVERT: X 536 LYS cc_start: 0.8734 (mttt) cc_final: 0.8318 (mttp) outliers start: 39 outliers final: 30 residues processed: 630 average time/residue: 0.2451 time to fit residues: 257.8321 Evaluate side-chains 569 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 539 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 559 HIS Chi-restraints excluded: chain C residue 559 HIS Chi-restraints excluded: chain D residue 559 HIS Chi-restraints excluded: chain E residue 559 HIS Chi-restraints excluded: chain F residue 559 HIS Chi-restraints excluded: chain G residue 559 HIS Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 559 HIS Chi-restraints excluded: chain I residue 559 HIS Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain K residue 559 HIS Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain L residue 559 HIS Chi-restraints excluded: chain M residue 559 HIS Chi-restraints excluded: chain N residue 559 HIS Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain O residue 559 HIS Chi-restraints excluded: chain P residue 559 HIS Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain Q residue 559 HIS Chi-restraints excluded: chain R residue 559 HIS Chi-restraints excluded: chain S residue 559 HIS Chi-restraints excluded: chain T residue 559 HIS Chi-restraints excluded: chain V residue 559 HIS Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 559 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 314 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 518 optimal weight: 8.9990 chunk 260 optimal weight: 0.9980 chunk 470 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 363 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 325 optimal weight: 0.1980 chunk 88 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 HIS A 559 HIS B 427 HIS B 559 HIS C 427 HIS C 559 HIS D 427 HIS D 559 HIS E 427 HIS E 559 HIS F 427 HIS F 559 HIS G 427 HIS G 559 HIS H 427 HIS H 559 HIS I 427 HIS I 559 HIS J 427 HIS K 427 HIS K 559 HIS L 427 HIS L 559 HIS M 427 HIS M 559 HIS N 427 HIS N 559 HIS O 427 HIS O 559 HIS P 427 HIS P 559 HIS Q 427 HIS Q 559 HIS R 427 HIS R 559 HIS S 427 HIS S 559 HIS T 427 HIS T 559 HIS V 427 HIS V 559 HIS W 427 HIS X 427 HIS Y 427 HIS Y 559 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.224152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.185033 restraints weight = 47130.728| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.86 r_work: 0.3902 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 46824 Z= 0.123 Angle : 0.455 5.506 63192 Z= 0.245 Chirality : 0.042 0.128 7296 Planarity : 0.004 0.037 8064 Dihedral : 3.413 11.151 6240 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.73 % Favored : 97.86 % Rotamer: Outliers : 1.84 % Allowed : 7.33 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.11), residues: 5880 helix: 2.69 (0.11), residues: 2136 sheet: 0.15 (0.15), residues: 1152 loop : -0.08 (0.13), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 450 TYR 0.001 0.000 TYR K 492 PHE 0.011 0.002 PHE X 560 TRP 0.009 0.001 TRP A 583 HIS 0.003 0.001 HIS Q 559 Details of bonding type rmsd covalent geometry : bond 0.00290 (46824) covalent geometry : angle 0.45457 (63192) hydrogen bonds : bond 0.03447 ( 2424) hydrogen bonds : angle 4.19456 ( 6912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 582 time to evaluate : 1.854 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: symmetry clash REVERT: I 385 MET cc_start: 0.4714 (ptt) cc_final: 0.4398 (mmm) REVERT: P 385 MET cc_start: 0.4746 (ptt) cc_final: 0.4408 (mmm) outliers start: 93 outliers final: 9 residues processed: 621 average time/residue: 0.2376 time to fit residues: 247.1635 Evaluate side-chains 478 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 469 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain X residue 528 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 499 optimal weight: 5.9990 chunk 468 optimal weight: 9.9990 chunk 305 optimal weight: 1.9990 chunk 441 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 368 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 396 optimal weight: 9.9990 chunk 375 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.213821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171482 restraints weight = 47297.827| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.47 r_work: 0.3669 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 46824 Z= 0.347 Angle : 0.708 6.184 63192 Z= 0.384 Chirality : 0.052 0.189 7296 Planarity : 0.006 0.048 8064 Dihedral : 4.373 15.708 6240 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.86 % Favored : 96.73 % Rotamer: Outliers : 1.72 % Allowed : 10.23 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.11), residues: 5880 helix: 1.63 (0.11), residues: 2280 sheet: -0.52 (0.14), residues: 1152 loop : -0.67 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 625 TYR 0.004 0.002 TYR E 492 PHE 0.021 0.004 PHE S 560 TRP 0.018 0.003 TRP Q 583 HIS 0.006 0.002 HIS R 424 Details of bonding type rmsd covalent geometry : bond 0.00877 (46824) covalent geometry : angle 0.70819 (63192) hydrogen bonds : bond 0.05674 ( 2424) hydrogen bonds : angle 4.83302 ( 6912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 486 time to evaluate : 1.675 Fit side-chains REVERT: A 473 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6796 (mtt) REVERT: A 486 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7517 (ttp-110) REVERT: B 385 MET cc_start: 0.5993 (mmm) cc_final: 0.5676 (mtm) REVERT: B 473 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6782 (mtt) REVERT: B 486 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7541 (ttp-110) REVERT: B 536 LYS cc_start: 0.8892 (mttt) cc_final: 0.8671 (mttm) REVERT: C 385 MET cc_start: 0.5963 (mmm) cc_final: 0.5747 (mtm) REVERT: C 473 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6754 (mtt) REVERT: C 486 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7548 (ttp-110) REVERT: D 473 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6786 (mtt) REVERT: D 486 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7547 (ttp-110) REVERT: D 536 LYS cc_start: 0.8860 (mttt) cc_final: 0.8597 (mttp) REVERT: E 473 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6803 (mtt) REVERT: E 486 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7557 (ttp-110) REVERT: E 536 LYS cc_start: 0.8904 (mttt) cc_final: 0.8668 (mttm) REVERT: F 473 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6763 (mtt) REVERT: F 486 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7567 (ttp-110) REVERT: F 536 LYS cc_start: 0.8834 (mttt) cc_final: 0.8596 (mttp) REVERT: G 473 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6772 (mtt) REVERT: G 486 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7549 (ttp-110) REVERT: G 536 LYS cc_start: 0.8894 (mttt) cc_final: 0.8674 (mttm) REVERT: H 473 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6770 (mtt) REVERT: H 486 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7541 (ttp-110) REVERT: I 473 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6797 (mtt) REVERT: I 486 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7525 (ttp-110) REVERT: J 473 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6781 (mtt) REVERT: J 486 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7535 (ttp-110) REVERT: K 473 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6736 (mtt) REVERT: K 486 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7532 (ttp-110) REVERT: L 473 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6791 (mtt) REVERT: L 486 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7535 (ttp-110) REVERT: M 473 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6726 (mtt) REVERT: M 486 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7564 (ttp-110) REVERT: M 536 LYS cc_start: 0.8866 (mttt) cc_final: 0.8602 (mttp) REVERT: N 473 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6745 (mtt) REVERT: N 486 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7568 (ttp-110) REVERT: N 536 LYS cc_start: 0.8907 (mttt) cc_final: 0.8685 (mttm) REVERT: O 473 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6794 (mtt) REVERT: O 486 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7536 (ttp-110) REVERT: P 473 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6801 (mtt) REVERT: P 486 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7548 (ttp-110) REVERT: Q 385 MET cc_start: 0.5983 (mmm) cc_final: 0.5658 (mtm) REVERT: Q 473 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6778 (mtt) REVERT: Q 486 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7552 (ttp-110) REVERT: Q 536 LYS cc_start: 0.8887 (mttt) cc_final: 0.8673 (mttm) REVERT: R 473 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6803 (mtt) REVERT: R 486 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7567 (ttp-110) REVERT: R 536 LYS cc_start: 0.8867 (mttt) cc_final: 0.8608 (mttp) REVERT: S 473 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6807 (mtt) REVERT: S 486 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7550 (ttp-110) REVERT: S 536 LYS cc_start: 0.8914 (mttt) cc_final: 0.8681 (mttm) REVERT: T 473 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6741 (mtt) REVERT: T 486 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7569 (ttp-110) REVERT: T 536 LYS cc_start: 0.8894 (mttt) cc_final: 0.8678 (mttm) REVERT: V 473 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6770 (mtt) REVERT: V 486 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7569 (ttp-110) REVERT: V 536 LYS cc_start: 0.8869 (mttt) cc_final: 0.8605 (mttp) REVERT: W 473 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6809 (mtt) REVERT: W 486 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7559 (ttp-110) REVERT: W 536 LYS cc_start: 0.8908 (mttt) cc_final: 0.8677 (mttm) REVERT: X 473 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6782 (mtt) REVERT: X 486 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7545 (ttp-110) REVERT: X 536 LYS cc_start: 0.8888 (mttt) cc_final: 0.8675 (mttm) REVERT: Y 473 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6797 (mtt) REVERT: Y 486 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7544 (ttp-110) REVERT: Y 536 LYS cc_start: 0.8870 (mttt) cc_final: 0.8613 (mttp) outliers start: 87 outliers final: 48 residues processed: 516 average time/residue: 0.2446 time to fit residues: 209.6387 Evaluate side-chains 544 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 472 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 513 VAL Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 410 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 410 ILE Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 513 VAL Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 410 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 456 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 530 optimal weight: 7.9990 chunk 517 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.218010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177506 restraints weight = 47097.888| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 1.82 r_work: 0.3757 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 46824 Z= 0.141 Angle : 0.504 5.985 63192 Z= 0.270 Chirality : 0.043 0.131 7296 Planarity : 0.005 0.047 8064 Dihedral : 3.750 12.063 6240 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.02 % Favored : 97.57 % Rotamer: Outliers : 1.80 % Allowed : 10.25 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.11), residues: 5880 helix: 1.90 (0.11), residues: 2280 sheet: -0.42 (0.14), residues: 1152 loop : -0.51 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 450 TYR 0.001 0.001 TYR F 492 PHE 0.013 0.002 PHE J 560 TRP 0.014 0.002 TRP R 583 HIS 0.002 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00339 (46824) covalent geometry : angle 0.50402 (63192) hydrogen bonds : bond 0.03767 ( 2424) hydrogen bonds : angle 4.31582 ( 6912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 482 time to evaluate : 1.425 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: A 473 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6918 (mtt) REVERT: A 486 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7539 (ttp-110) REVERT: B 473 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6974 (mtt) REVERT: B 486 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7572 (ttp-110) REVERT: C 473 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6978 (mtt) REVERT: C 486 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7542 (ttp-110) REVERT: D 473 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7012 (mtt) REVERT: D 486 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7558 (ttp-110) REVERT: E 473 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6975 (mtt) REVERT: E 486 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7593 (ttp-110) REVERT: F 473 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6978 (mtt) REVERT: F 486 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7559 (ttp-110) REVERT: G 473 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6977 (mtt) REVERT: G 486 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7579 (ttp-110) REVERT: H 473 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6981 (mtt) REVERT: H 486 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7572 (ttp-110) REVERT: I 473 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6907 (mtt) REVERT: I 486 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7539 (ttp-110) REVERT: J 473 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6970 (mtt) REVERT: J 486 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7560 (ttp-110) REVERT: K 473 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6964 (mtt) REVERT: K 486 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7550 (ttp-110) REVERT: L 473 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6919 (mtt) REVERT: L 486 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7546 (ttp-110) REVERT: M 473 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6968 (mtt) REVERT: M 486 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7553 (ttp-110) REVERT: N 473 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6987 (mtt) REVERT: N 486 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7595 (ttp-110) REVERT: O 473 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6961 (mtt) REVERT: O 486 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7522 (ttp-110) REVERT: P 473 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6929 (mtt) REVERT: P 486 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7558 (ttp-110) REVERT: Q 473 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6955 (mtt) REVERT: Q 486 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7558 (ttp-110) REVERT: R 473 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6997 (mtt) REVERT: R 486 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7553 (ttp-110) REVERT: S 473 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6978 (mtt) REVERT: S 486 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7527 (ttp-110) REVERT: T 473 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6960 (mtt) REVERT: T 486 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7551 (ttp-110) REVERT: V 473 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6979 (mtt) REVERT: V 486 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7529 (ttp-110) REVERT: W 473 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6980 (mtt) REVERT: W 486 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7560 (ttp-110) REVERT: X 473 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6959 (mtt) REVERT: X 486 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7553 (ttp-110) REVERT: Y 473 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6935 (mtt) REVERT: Y 486 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7548 (ttp-110) outliers start: 91 outliers final: 24 residues processed: 525 average time/residue: 0.2382 time to fit residues: 209.5534 Evaluate side-chains 502 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 454 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 149 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 497 optimal weight: 0.0050 chunk 370 optimal weight: 30.0000 chunk 140 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 493 optimal weight: 10.0000 chunk 435 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.218811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.175019 restraints weight = 45936.654| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.20 r_work: 0.3735 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 46824 Z= 0.121 Angle : 0.458 5.302 63192 Z= 0.247 Chirality : 0.042 0.128 7296 Planarity : 0.005 0.045 8064 Dihedral : 3.533 11.860 6240 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.43 % Favored : 97.16 % Rotamer: Outliers : 1.22 % Allowed : 12.22 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.11), residues: 5880 helix: 2.19 (0.11), residues: 2280 sheet: -0.34 (0.14), residues: 1152 loop : -0.42 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 450 TYR 0.001 0.001 TYR I 492 PHE 0.012 0.002 PHE X 613 TRP 0.012 0.001 TRP S 583 HIS 0.002 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00291 (46824) covalent geometry : angle 0.45833 (63192) hydrogen bonds : bond 0.03561 ( 2424) hydrogen bonds : angle 4.12038 ( 6912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 513 time to evaluate : 1.535 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: symmetry clash REVERT: A 473 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6754 (mtt) REVERT: A 486 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7555 (ttp-110) REVERT: B 473 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6769 (mtt) REVERT: B 486 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7571 (ttp-110) REVERT: C 473 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6764 (mtt) REVERT: C 486 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7564 (ttp-110) REVERT: D 473 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6787 (mtt) REVERT: D 486 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7545 (ttp-110) REVERT: E 473 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6784 (mtt) REVERT: E 486 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7555 (ttp-110) REVERT: F 473 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6753 (mtt) REVERT: F 486 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7536 (ttp-110) REVERT: G 473 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6793 (mtt) REVERT: G 486 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7524 (ttp-110) REVERT: H 473 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6754 (mtt) REVERT: H 486 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7569 (ttp-110) REVERT: I 473 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6799 (mtt) REVERT: I 486 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7530 (ttp-110) REVERT: J 473 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6745 (mtt) REVERT: J 486 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7544 (ttp-110) REVERT: K 473 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6736 (mtt) REVERT: K 486 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7560 (ttp-110) REVERT: L 473 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6752 (mtt) REVERT: L 486 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7570 (ttp-110) REVERT: M 473 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6765 (mtt) REVERT: M 486 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7518 (ttp-110) REVERT: N 473 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6775 (mtt) REVERT: N 486 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7574 (ttp-110) REVERT: O 473 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6766 (mtt) REVERT: O 486 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7554 (ttp-110) REVERT: P 473 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6793 (mtt) REVERT: P 486 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7569 (ttp-110) REVERT: Q 473 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6773 (mtt) REVERT: Q 486 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7575 (ttp-110) REVERT: R 473 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6800 (mtt) REVERT: R 486 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7518 (ttp-110) REVERT: S 473 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6762 (mtt) REVERT: S 486 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7548 (ttp-110) REVERT: T 473 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6761 (mtt) REVERT: T 486 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7565 (ttp-110) REVERT: V 473 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6740 (mtt) REVERT: V 486 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7547 (ttp-110) REVERT: W 421 MET cc_start: 0.8183 (mtt) cc_final: 0.7887 (mtt) REVERT: W 473 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6771 (mtt) REVERT: W 486 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7559 (ttp-110) REVERT: X 473 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6747 (mtt) REVERT: X 486 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7573 (ttp-110) REVERT: Y 473 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6801 (mtt) REVERT: Y 486 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7538 (ttp-110) outliers start: 62 outliers final: 36 residues processed: 525 average time/residue: 0.2296 time to fit residues: 201.0830 Evaluate side-chains 515 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 455 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 410 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 410 ILE Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 410 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 492 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 255 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 37 optimal weight: 0.0030 chunk 362 optimal weight: 8.9990 chunk 428 optimal weight: 0.0270 chunk 348 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 overall best weight: 1.1250 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.220811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.177732 restraints weight = 46848.709| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.02 r_work: 0.3823 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 46824 Z= 0.103 Angle : 0.436 5.210 63192 Z= 0.234 Chirality : 0.042 0.127 7296 Planarity : 0.004 0.044 8064 Dihedral : 3.403 12.908 6240 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.53 % Favored : 98.06 % Rotamer: Outliers : 1.38 % Allowed : 12.70 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.11), residues: 5880 helix: 2.45 (0.11), residues: 2280 sheet: -0.18 (0.14), residues: 1152 loop : -0.26 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 450 TYR 0.001 0.000 TYR D 492 PHE 0.012 0.001 PHE P 613 TRP 0.011 0.001 TRP F 583 HIS 0.001 0.000 HIS I 424 Details of bonding type rmsd covalent geometry : bond 0.00246 (46824) covalent geometry : angle 0.43556 (63192) hydrogen bonds : bond 0.03310 ( 2424) hydrogen bonds : angle 3.95399 ( 6912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 503 time to evaluate : 1.885 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: symmetry clash REVERT: A 435 GLU cc_start: 0.6839 (pm20) cc_final: 0.6578 (pm20) REVERT: A 473 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6813 (mtt) REVERT: A 486 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7545 (ttp-110) REVERT: B 421 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7799 (mpp) REVERT: B 473 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6933 (mtt) REVERT: B 486 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7546 (ttp-110) REVERT: C 473 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6842 (mtt) REVERT: C 486 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7532 (ttp-110) REVERT: D 435 GLU cc_start: 0.6814 (pm20) cc_final: 0.6558 (pm20) REVERT: D 473 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6861 (mtt) REVERT: D 486 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7483 (ttp-110) REVERT: E 435 GLU cc_start: 0.6787 (pm20) cc_final: 0.6534 (pm20) REVERT: E 473 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6850 (mtt) REVERT: E 486 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7511 (ttp-110) REVERT: F 473 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6829 (mtt) REVERT: F 486 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7569 (ttp-110) REVERT: G 473 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6946 (mtt) REVERT: G 486 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7519 (ttp-110) REVERT: H 473 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6933 (mtt) REVERT: H 486 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7583 (ttp-110) REVERT: I 473 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6937 (mtt) REVERT: I 486 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7467 (ttp-110) REVERT: J 435 GLU cc_start: 0.6810 (pm20) cc_final: 0.6553 (pm20) REVERT: J 473 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6812 (mtt) REVERT: J 486 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7545 (ttp-110) REVERT: K 421 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7739 (mpp) REVERT: K 435 GLU cc_start: 0.6838 (pm20) cc_final: 0.6580 (pm20) REVERT: K 473 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6817 (mtt) REVERT: K 486 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7506 (ttp-110) REVERT: L 435 GLU cc_start: 0.6847 (pm20) cc_final: 0.6588 (pm20) REVERT: L 473 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6921 (mtt) REVERT: L 486 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7543 (ttp-110) REVERT: M 473 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6875 (mtt) REVERT: M 486 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7501 (ttp-110) REVERT: N 473 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6871 (mtt) REVERT: N 486 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7499 (ttp-110) REVERT: O 435 GLU cc_start: 0.6847 (pm20) cc_final: 0.6586 (pm20) REVERT: O 473 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6802 (mtt) REVERT: O 486 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7480 (ttp-110) REVERT: P 473 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6960 (mtt) REVERT: P 486 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7534 (ttp-110) REVERT: Q 473 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6799 (mtt) REVERT: Q 486 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7565 (ttp-110) REVERT: R 435 GLU cc_start: 0.6815 (pm20) cc_final: 0.6558 (pm20) REVERT: R 473 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6847 (mtt) REVERT: R 486 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7543 (ttp-110) REVERT: R 531 LYS cc_start: 0.7302 (tttt) cc_final: 0.7060 (ttmt) REVERT: S 435 GLU cc_start: 0.6806 (pm20) cc_final: 0.6548 (pm20) REVERT: S 473 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6938 (mtt) REVERT: S 486 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7515 (ttp-110) REVERT: T 473 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6815 (mtt) REVERT: T 486 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7559 (ttp-110) REVERT: V 473 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6919 (mtt) REVERT: V 486 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7564 (ttp-110) REVERT: W 421 MET cc_start: 0.8256 (mtt) cc_final: 0.7848 (mtt) REVERT: W 473 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6827 (mtt) REVERT: W 486 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7563 (ttp-110) REVERT: X 473 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6816 (mtt) REVERT: X 486 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7493 (ttp-110) REVERT: Y 473 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6948 (mtt) REVERT: Y 486 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7552 (ttp-110) outliers start: 70 outliers final: 28 residues processed: 517 average time/residue: 0.2413 time to fit residues: 207.1376 Evaluate side-chains 521 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 467 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 421 MET Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 395 optimal weight: 7.9990 chunk 521 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 422 optimal weight: 10.0000 chunk 542 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 333 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.216161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.177340 restraints weight = 47702.706| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.06 r_work: 0.3719 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 46824 Z= 0.253 Angle : 0.577 5.493 63192 Z= 0.313 Chirality : 0.047 0.137 7296 Planarity : 0.005 0.045 8064 Dihedral : 3.939 12.980 6240 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.96 % Favored : 96.63 % Rotamer: Outliers : 2.21 % Allowed : 11.93 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.11), residues: 5880 helix: 1.91 (0.11), residues: 2280 sheet: -0.56 (0.14), residues: 1152 loop : -0.48 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 417 TYR 0.003 0.001 TYR V 492 PHE 0.016 0.003 PHE J 560 TRP 0.012 0.002 TRP N 583 HIS 0.004 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00643 (46824) covalent geometry : angle 0.57710 (63192) hydrogen bonds : bond 0.04760 ( 2424) hydrogen bonds : angle 4.38837 ( 6912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 462 time to evaluate : 1.348 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 473 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6916 (mtt) REVERT: A 486 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7536 (ttp-110) REVERT: B 421 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7888 (mpp) REVERT: B 473 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6918 (mtt) REVERT: B 486 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7567 (ttp-110) REVERT: C 407 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5522 (tp) REVERT: C 421 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8265 (mtt) REVERT: C 473 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6919 (mtt) REVERT: C 486 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7523 (ttp-110) REVERT: D 407 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5482 (tp) REVERT: D 473 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6952 (mtt) REVERT: D 486 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7542 (ttp-110) REVERT: E 407 ILE cc_start: 0.5913 (OUTLIER) cc_final: 0.5537 (tp) REVERT: E 473 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6960 (mtt) REVERT: E 486 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7539 (ttp-110) REVERT: F 407 ILE cc_start: 0.5958 (OUTLIER) cc_final: 0.5585 (tp) REVERT: F 473 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6914 (mtt) REVERT: F 486 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7544 (ttp-110) REVERT: G 407 ILE cc_start: 0.5911 (OUTLIER) cc_final: 0.5539 (tp) REVERT: G 473 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6909 (mtt) REVERT: G 486 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7559 (ttp-110) REVERT: H 473 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6918 (mtt) REVERT: H 486 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7616 (ttp-110) REVERT: I 407 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5533 (tp) REVERT: I 421 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8257 (mtt) REVERT: I 473 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6920 (mtt) REVERT: I 486 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7603 (ttp-110) REVERT: J 407 ILE cc_start: 0.5975 (OUTLIER) cc_final: 0.5595 (tp) REVERT: J 421 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8176 (mtt) REVERT: J 473 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6922 (mtt) REVERT: J 486 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7615 (ttp-110) REVERT: K 407 ILE cc_start: 0.5964 (OUTLIER) cc_final: 0.5578 (tp) REVERT: K 421 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7888 (mpp) REVERT: K 473 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6905 (mtt) REVERT: K 486 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7619 (ttp-110) REVERT: L 473 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6926 (mtt) REVERT: L 486 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7538 (ttp-110) REVERT: M 473 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6900 (mtt) REVERT: M 486 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7520 (ttp-110) REVERT: N 407 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.5523 (tp) REVERT: N 473 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6933 (mtt) REVERT: N 486 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7558 (ttp-110) REVERT: O 473 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6920 (mtt) REVERT: O 486 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7531 (ttp-110) REVERT: P 473 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6935 (mtt) REVERT: P 486 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7517 (ttp-110) REVERT: Q 473 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6912 (mtt) REVERT: Q 486 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7543 (ttp-110) REVERT: R 407 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5477 (tp) REVERT: R 473 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6938 (mtt) REVERT: R 486 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7536 (ttp-110) REVERT: S 407 ILE cc_start: 0.5916 (OUTLIER) cc_final: 0.5540 (tp) REVERT: S 473 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6946 (mtt) REVERT: S 486 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7534 (ttp-110) REVERT: T 407 ILE cc_start: 0.5903 (OUTLIER) cc_final: 0.5533 (tp) REVERT: T 473 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: T 486 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7547 (ttp-110) REVERT: V 473 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6901 (mtt) REVERT: V 486 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7514 (ttp-110) REVERT: W 421 MET cc_start: 0.8357 (mtt) cc_final: 0.8008 (mtt) REVERT: W 473 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6942 (mtt) REVERT: W 486 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7520 (ttp-110) REVERT: X 473 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6919 (mtt) REVERT: X 486 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7543 (ttp-110) REVERT: Y 407 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5455 (tp) REVERT: Y 473 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6934 (mtt) REVERT: Y 486 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7547 (ttp-110) outliers start: 112 outliers final: 45 residues processed: 518 average time/residue: 0.2409 time to fit residues: 206.7468 Evaluate side-chains 549 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 462 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 421 MET Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 407 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 421 MET Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 407 ILE Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 410 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain R residue 513 VAL Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 407 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 407 ILE Chi-restraints excluded: chain T residue 410 ILE Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 410 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 407 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 513 VAL Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 183 optimal weight: 7.9990 chunk 498 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 388 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 526 optimal weight: 0.8980 chunk 278 optimal weight: 3.9990 chunk 512 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN B 442 GLN C 442 GLN D 442 GLN E 442 GLN F 442 GLN G 442 GLN H 442 GLN I 442 GLN J 442 GLN K 442 GLN L 442 GLN M 442 GLN N 442 GLN O 442 GLN P 442 GLN Q 442 GLN R 442 GLN S 442 GLN T 442 GLN V 442 GLN W 442 GLN X 442 GLN Y 442 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.221570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.178601 restraints weight = 45431.625| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.05 r_work: 0.3776 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 46824 Z= 0.093 Angle : 0.426 5.013 63192 Z= 0.230 Chirality : 0.042 0.131 7296 Planarity : 0.004 0.044 8064 Dihedral : 3.409 11.980 6240 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.70 % Favored : 97.89 % Rotamer: Outliers : 2.01 % Allowed : 12.40 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.11), residues: 5880 helix: 2.40 (0.11), residues: 2280 sheet: -0.27 (0.14), residues: 1152 loop : -0.26 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 417 TYR 0.001 0.000 TYR H 492 PHE 0.012 0.001 PHE K 613 TRP 0.011 0.001 TRP W 583 HIS 0.001 0.000 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00213 (46824) covalent geometry : angle 0.42647 (63192) hydrogen bonds : bond 0.03254 ( 2424) hydrogen bonds : angle 3.96984 ( 6912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 493 time to evaluate : 1.314 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 421 MET cc_start: 0.8735 (tpp) cc_final: 0.8392 (tpp) REVERT: A 435 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: A 473 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6821 (mtt) REVERT: A 486 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7561 (ttp-110) REVERT: B 407 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5341 (tp) REVERT: B 421 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7788 (mpp) REVERT: B 473 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6841 (mtt) REVERT: B 486 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7566 (ttp-110) REVERT: C 421 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7988 (mtt) REVERT: C 473 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6814 (mtt) REVERT: C 486 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7553 (ttp-110) REVERT: D 435 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6576 (pm20) REVERT: D 473 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6808 (mtt) REVERT: D 486 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7559 (ttp-110) REVERT: D 531 LYS cc_start: 0.7220 (tttt) cc_final: 0.7016 (ttmt) REVERT: E 421 MET cc_start: 0.8753 (tpp) cc_final: 0.8396 (tpp) REVERT: E 435 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: E 473 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6796 (mtt) REVERT: E 486 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7551 (ttp-110) REVERT: F 473 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6809 (mtt) REVERT: F 486 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7548 (ttp-110) REVERT: G 473 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6835 (mtt) REVERT: G 486 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7553 (ttp-110) REVERT: H 407 ILE cc_start: 0.5634 (OUTLIER) cc_final: 0.5260 (tp) REVERT: H 473 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6807 (mtt) REVERT: H 486 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7554 (ttp-110) REVERT: I 421 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8000 (mtt) REVERT: I 473 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6869 (mtt) REVERT: I 486 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7531 (ttp-110) REVERT: J 435 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6574 (pm20) REVERT: J 473 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6804 (mtt) REVERT: J 486 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7525 (ttp-110) REVERT: K 421 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7807 (mpp) REVERT: K 435 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6584 (pm20) REVERT: K 473 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6794 (mtt) REVERT: K 486 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7565 (ttp-110) REVERT: L 421 MET cc_start: 0.8727 (tpp) cc_final: 0.8368 (tpp) REVERT: L 435 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6574 (pm20) REVERT: L 473 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6811 (mtt) REVERT: L 486 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7561 (ttp-110) REVERT: M 407 ILE cc_start: 0.5627 (OUTLIER) cc_final: 0.5244 (tp) REVERT: M 473 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6805 (mtt) REVERT: M 486 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7541 (ttp-110) REVERT: M 531 LYS cc_start: 0.7216 (tttt) cc_final: 0.7004 (ttmt) REVERT: N 473 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6817 (mtt) REVERT: N 486 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7553 (ttp-110) REVERT: O 421 MET cc_start: 0.8737 (tpp) cc_final: 0.8382 (tpp) REVERT: O 435 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6562 (pm20) REVERT: O 473 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6824 (mtt) REVERT: O 486 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7563 (ttp-110) REVERT: P 407 ILE cc_start: 0.5621 (OUTLIER) cc_final: 0.5246 (tp) REVERT: P 473 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6859 (mtt) REVERT: P 486 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7516 (ttp-110) REVERT: Q 407 ILE cc_start: 0.5397 (OUTLIER) cc_final: 0.5029 (tp) REVERT: Q 473 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6814 (mtt) REVERT: Q 486 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7583 (ttp-110) REVERT: R 435 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: R 473 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6818 (mtt) REVERT: R 486 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7551 (ttp-110) REVERT: R 536 LYS cc_start: 0.8348 (mttm) cc_final: 0.8032 (mtmm) REVERT: S 421 MET cc_start: 0.8745 (tpp) cc_final: 0.8384 (tpp) REVERT: S 435 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: S 473 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6800 (mtt) REVERT: S 486 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7538 (ttp-110) REVERT: T 473 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6813 (mtt) REVERT: T 486 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7559 (ttp-110) REVERT: V 407 ILE cc_start: 0.5629 (OUTLIER) cc_final: 0.5245 (tp) REVERT: V 473 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6782 (mtt) REVERT: V 486 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7549 (ttp-110) REVERT: W 421 MET cc_start: 0.8221 (mtt) cc_final: 0.7773 (mtt) REVERT: W 473 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6807 (mtt) REVERT: W 486 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7565 (ttp-110) REVERT: X 407 ILE cc_start: 0.5386 (OUTLIER) cc_final: 0.5017 (tp) REVERT: X 473 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6831 (mtt) REVERT: X 486 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7574 (ttp-110) REVERT: Y 473 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6809 (mtt) REVERT: Y 486 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7565 (ttp-110) outliers start: 102 outliers final: 55 residues processed: 532 average time/residue: 0.2177 time to fit residues: 192.1516 Evaluate side-chains 568 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 469 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 442 GLN Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 442 GLN Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 442 GLN Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 435 GLU Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 421 MET Chi-restraints excluded: chain K residue 435 GLU Chi-restraints excluded: chain K residue 442 GLN Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 435 GLU Chi-restraints excluded: chain L residue 442 GLN Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 442 GLN Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 442 GLN Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 442 GLN Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 407 ILE Chi-restraints excluded: chain P residue 442 GLN Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 407 ILE Chi-restraints excluded: chain Q residue 442 GLN Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 442 GLN Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain S residue 435 GLU Chi-restraints excluded: chain S residue 442 GLN Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 407 ILE Chi-restraints excluded: chain V residue 442 GLN Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 442 GLN Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 407 ILE Chi-restraints excluded: chain X residue 442 GLN Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 442 GLN Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 400 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 407 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 285 optimal weight: 0.6980 chunk 318 optimal weight: 8.9990 chunk 399 optimal weight: 8.9990 chunk 460 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 chunk 294 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN B 442 GLN E 442 GLN L 442 GLN O 442 GLN Q 442 GLN S 442 GLN W 442 GLN X 442 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.219840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.176018 restraints weight = 45749.084| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.26 r_work: 0.3739 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 46824 Z= 0.116 Angle : 0.442 5.138 63192 Z= 0.238 Chirality : 0.042 0.127 7296 Planarity : 0.004 0.044 8064 Dihedral : 3.419 12.901 6240 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.30 % Favored : 97.30 % Rotamer: Outliers : 2.23 % Allowed : 11.81 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.11), residues: 5880 helix: 2.47 (0.11), residues: 2280 sheet: -0.17 (0.14), residues: 1152 loop : -0.19 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 450 TYR 0.001 0.001 TYR P 492 PHE 0.012 0.001 PHE K 613 TRP 0.011 0.001 TRP F 583 HIS 0.002 0.001 HIS L 424 Details of bonding type rmsd covalent geometry : bond 0.00279 (46824) covalent geometry : angle 0.44195 (63192) hydrogen bonds : bond 0.03482 ( 2424) hydrogen bonds : angle 3.97357 ( 6912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 471 time to evaluate : 1.203 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 407 ILE cc_start: 0.5680 (OUTLIER) cc_final: 0.5293 (tp) REVERT: A 421 MET cc_start: 0.8726 (tpp) cc_final: 0.8390 (tpp) REVERT: A 435 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6626 (pm20) REVERT: A 473 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6857 (mtt) REVERT: A 486 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7539 (ttp-110) REVERT: B 407 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.5293 (tp) REVERT: B 421 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7771 (mpp) REVERT: B 473 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6875 (mtt) REVERT: B 486 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7569 (ttp-110) REVERT: C 421 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7979 (mtt) REVERT: C 473 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6863 (mtt) REVERT: C 486 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7553 (ttp-110) REVERT: D 435 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: D 473 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6911 (mtt) REVERT: D 486 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7539 (ttp-110) REVERT: E 421 MET cc_start: 0.8740 (tpp) cc_final: 0.8391 (tpp) REVERT: E 435 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6605 (pm20) REVERT: E 473 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6824 (mtt) REVERT: E 486 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7546 (ttp-110) REVERT: F 473 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6868 (mtt) REVERT: F 486 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7543 (ttp-110) REVERT: G 473 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6866 (mtt) REVERT: G 486 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7560 (ttp-110) REVERT: H 407 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5216 (tp) REVERT: H 473 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6846 (mtt) REVERT: H 486 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7555 (ttp-110) REVERT: I 421 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7981 (mtt) REVERT: I 473 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6827 (mtt) REVERT: I 486 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7531 (ttp-110) REVERT: J 421 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7833 (mpp) REVERT: J 435 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: J 473 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6859 (mtt) REVERT: J 486 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7518 (ttp-110) REVERT: K 421 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7762 (mpp) REVERT: K 435 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: K 473 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6871 (mtt) REVERT: K 486 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7554 (ttp-110) REVERT: L 407 ILE cc_start: 0.5674 (OUTLIER) cc_final: 0.5285 (tp) REVERT: L 421 MET cc_start: 0.8719 (tpp) cc_final: 0.8366 (tpp) REVERT: L 435 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: L 473 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6854 (mtt) REVERT: L 486 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7548 (ttp-110) REVERT: M 407 ILE cc_start: 0.5598 (OUTLIER) cc_final: 0.5207 (tp) REVERT: M 473 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6854 (mtt) REVERT: M 486 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7534 (ttp-110) REVERT: N 473 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6866 (mtt) REVERT: N 486 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7562 (ttp-110) REVERT: O 407 ILE cc_start: 0.5672 (OUTLIER) cc_final: 0.5286 (tp) REVERT: O 421 MET cc_start: 0.8730 (tpp) cc_final: 0.8382 (tpp) REVERT: O 435 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: O 473 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6854 (mtt) REVERT: O 486 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7537 (ttp-110) REVERT: P 407 ILE cc_start: 0.5601 (OUTLIER) cc_final: 0.5216 (tp) REVERT: P 473 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6824 (mtt) REVERT: P 486 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7520 (ttp-110) REVERT: Q 407 ILE cc_start: 0.5570 (OUTLIER) cc_final: 0.5195 (tp) REVERT: Q 473 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6896 (mtt) REVERT: Q 486 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7574 (ttp-110) REVERT: R 435 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: R 473 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6906 (mtt) REVERT: R 486 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7539 (ttp-110) REVERT: S 421 MET cc_start: 0.8743 (tpp) cc_final: 0.8391 (tpp) REVERT: S 435 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: S 473 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6824 (mtt) REVERT: S 486 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7519 (ttp-110) REVERT: T 473 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6861 (mtt) REVERT: T 486 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7561 (ttp-110) REVERT: V 407 ILE cc_start: 0.5601 (OUTLIER) cc_final: 0.5209 (tp) REVERT: V 473 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6844 (mtt) REVERT: V 486 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7529 (ttp-110) REVERT: W 407 ILE cc_start: 0.5615 (OUTLIER) cc_final: 0.5235 (tp) REVERT: W 421 MET cc_start: 0.8200 (mtt) cc_final: 0.7757 (mtt) REVERT: W 473 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6862 (mtt) REVERT: W 486 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7535 (ttp-110) REVERT: X 407 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5188 (tp) REVERT: X 473 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6911 (mtt) REVERT: X 486 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7557 (ttp-110) REVERT: Y 473 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6869 (mtt) REVERT: Y 486 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7555 (ttp-110) outliers start: 113 outliers final: 59 residues processed: 523 average time/residue: 0.2123 time to fit residues: 184.2447 Evaluate side-chains 579 residues out of total 5064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 471 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 442 GLN Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 442 GLN Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 421 MET Chi-restraints excluded: chain I residue 442 GLN Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 421 MET Chi-restraints excluded: chain J residue 435 GLU Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 421 MET Chi-restraints excluded: chain K residue 435 GLU Chi-restraints excluded: chain K residue 442 GLN Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 407 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 435 GLU Chi-restraints excluded: chain L residue 442 GLN Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 442 GLN Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 442 GLN Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 407 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 435 GLU Chi-restraints excluded: chain O residue 442 GLN Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 407 ILE Chi-restraints excluded: chain P residue 442 GLN Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 407 ILE Chi-restraints excluded: chain Q residue 442 GLN Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 442 GLN Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 435 GLU Chi-restraints excluded: chain S residue 442 GLN Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 407 ILE Chi-restraints excluded: chain V residue 442 GLN Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 407 ILE Chi-restraints excluded: chain W residue 442 GLN Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 407 ILE Chi-restraints excluded: chain X residue 442 GLN Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 442 GLN Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 435 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 545 optimal weight: 0.0770 chunk 474 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 361 optimal weight: 20.0000 chunk 338 optimal weight: 30.0000 chunk 171 optimal weight: 4.9990 chunk 269 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN B 442 GLN C 442 GLN D 442 GLN E 442 GLN F 442 GLN G 442 GLN H 442 GLN I 442 GLN J 442 GLN K 442 GLN L 442 GLN M 442 GLN N 442 GLN O 442 GLN P 442 GLN Q 442 GLN R 442 GLN S 442 GLN T 442 GLN V 442 GLN W 442 GLN X 442 GLN Y 442 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.222227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.177465 restraints weight = 45557.859| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.41 r_work: 0.3724 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 46824 Z= 0.094 Angle : 0.422 5.019 63192 Z= 0.227 Chirality : 0.042 0.138 7296 Planarity : 0.004 0.043 8064 Dihedral : 3.329 14.684 6240 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.17 % Favored : 98.42 % Rotamer: Outliers : 2.05 % Allowed : 12.11 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.11), residues: 5880 helix: 2.58 (0.11), residues: 2280 sheet: -0.00 (0.14), residues: 1152 loop : 0.00 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 440 TYR 0.001 0.000 TYR E 492 PHE 0.012 0.001 PHE O 613 TRP 0.010 0.001 TRP F 583 HIS 0.001 0.000 HIS F 424 Details of bonding type rmsd covalent geometry : bond 0.00215 (46824) covalent geometry : angle 0.42241 (63192) hydrogen bonds : bond 0.03237 ( 2424) hydrogen bonds : angle 3.87049 ( 6912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8154.60 seconds wall clock time: 140 minutes 44.36 seconds (8444.36 seconds total)