Starting phenix.real_space_refine on Tue Jul 7 02:23:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0y_66449/07_2026/9x0y_66449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0y_66449/07_2026/9x0y_66449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0y_66449/07_2026/9x0y_66449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0y_66449/07_2026/9x0y_66449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0y_66449/07_2026/9x0y_66449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0y_66449/07_2026/9x0y_66449.map" } resolution = 2.68 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= 0.002 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 154 5.16 5 C 26362 2.51 5 N 6958 2.21 5 O 7966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41454 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 17, 'TRANS': 293} Chain breaks: 2 Chain: "O" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, P, Q, R, S, T, U, V, W, X, Y, Z, a, b Time building chain proxies: 4.54, per 1000 atoms: 0.11 Number of scatterers: 41454 At special positions: 0 Unit cell: (172.53, 175.77, 137.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 14 15.00 O 7966 8.00 N 6958 7.00 C 26362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS O 101 " - pdb=" SG CYS O 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 499 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS E 506 " distance=2.03 Simple disulfide: pdb=" SG CYS F 499 " - pdb=" SG CYS F 506 " distance=2.03 Simple disulfide: pdb=" SG CYS G 499 " - pdb=" SG CYS G 506 " distance=2.03 Simple disulfide: pdb=" SG CYS H 499 " - pdb=" SG CYS H 506 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS I 506 " distance=2.03 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 506 " distance=2.03 Simple disulfide: pdb=" SG CYS K 499 " - pdb=" SG CYS K 506 " distance=2.03 Simple disulfide: pdb=" SG CYS L 499 " - pdb=" SG CYS L 506 " distance=2.03 Simple disulfide: pdb=" SG CYS M 499 " - pdb=" SG CYS M 506 " distance=2.03 Simple disulfide: pdb=" SG CYS N 499 " - pdb=" SG CYS N 506 " distance=2.03 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 101 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS S 101 " - pdb=" SG CYS S 104 " distance=2.03 Simple disulfide: pdb=" SG CYS T 101 " - pdb=" SG CYS T 104 " distance=2.03 Simple disulfide: pdb=" SG CYS U 101 " - pdb=" SG CYS U 104 " distance=2.03 Simple disulfide: pdb=" SG CYS V 101 " - pdb=" SG CYS V 104 " distance=2.03 Simple disulfide: pdb=" SG CYS W 101 " - pdb=" SG CYS W 104 " distance=2.03 Simple disulfide: pdb=" SG CYS X 101 " - pdb=" SG CYS X 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 101 " - pdb=" SG CYS Y 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 101 " - pdb=" SG CYS Z 104 " distance=2.03 Simple disulfide: pdb=" SG CYS a 101 " - pdb=" SG CYS a 104 " distance=2.03 Simple disulfide: pdb=" SG CYS b 101 " - pdb=" SG CYS b 104 " distance=2.03 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: 3.59 Conformation dependent library (CDL) restraints added in 2.1 seconds 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9800 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 58 sheets defined 24.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 429 through 444 Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG A 682 " --> pdb=" O TYR A 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA O 46 " --> pdb=" O PRO O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 72 Processing helix chain 'O' and resid 72 through 79 Processing helix chain 'O' and resid 81 through 90 Processing helix chain 'O' and resid 90 through 99 removed outlier: 3.544A pdb=" N GLU O 96 " --> pdb=" O ASP O 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA P 46 " --> pdb=" O PRO P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 72 Processing helix chain 'P' and resid 72 through 79 Processing helix chain 'P' and resid 81 through 90 Processing helix chain 'P' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU P 96 " --> pdb=" O ASP P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.748A pdb=" N ALA Q 46 " --> pdb=" O PRO Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 72 Processing helix chain 'Q' and resid 72 through 79 Processing helix chain 'Q' and resid 81 through 90 Processing helix chain 'Q' and resid 90 through 99 removed outlier: 3.542A pdb=" N GLU Q 96 " --> pdb=" O ASP Q 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 53 removed outlier: 3.748A pdb=" N ALA R 46 " --> pdb=" O PRO R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 72 Processing helix chain 'R' and resid 72 through 79 Processing helix chain 'R' and resid 81 through 90 Processing helix chain 'R' and resid 90 through 99 removed outlier: 3.544A pdb=" N GLU R 96 " --> pdb=" O ASP R 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA S 46 " --> pdb=" O PRO S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 72 Processing helix chain 'S' and resid 72 through 79 Processing helix chain 'S' and resid 81 through 90 Processing helix chain 'S' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU S 96 " --> pdb=" O ASP S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA T 46 " --> pdb=" O PRO T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 72 Processing helix chain 'T' and resid 72 through 79 Processing helix chain 'T' and resid 81 through 90 Processing helix chain 'T' and resid 90 through 99 removed outlier: 3.544A pdb=" N GLU T 96 " --> pdb=" O ASP T 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA U 46 " --> pdb=" O PRO U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 72 Processing helix chain 'U' and resid 72 through 79 Processing helix chain 'U' and resid 81 through 90 Processing helix chain 'U' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU U 96 " --> pdb=" O ASP U 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 53 removed outlier: 3.748A pdb=" N ALA V 46 " --> pdb=" O PRO V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 72 Processing helix chain 'V' and resid 72 through 79 Processing helix chain 'V' and resid 81 through 90 Processing helix chain 'V' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU V 96 " --> pdb=" O ASP V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA W 46 " --> pdb=" O PRO W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 72 Processing helix chain 'W' and resid 72 through 79 Processing helix chain 'W' and resid 81 through 90 Processing helix chain 'W' and resid 90 through 99 removed outlier: 3.544A pdb=" N GLU W 96 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA X 46 " --> pdb=" O PRO X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 72 Processing helix chain 'X' and resid 72 through 79 Processing helix chain 'X' and resid 81 through 90 Processing helix chain 'X' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU X 96 " --> pdb=" O ASP X 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 53 removed outlier: 3.748A pdb=" N ALA Y 46 " --> pdb=" O PRO Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 72 Processing helix chain 'Y' and resid 72 through 79 Processing helix chain 'Y' and resid 81 through 90 Processing helix chain 'Y' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU Y 96 " --> pdb=" O ASP Y 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 72 Processing helix chain 'Z' and resid 72 through 79 Processing helix chain 'Z' and resid 81 through 90 Processing helix chain 'Z' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU Z 96 " --> pdb=" O ASP Z 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 53 removed outlier: 3.748A pdb=" N ALA a 46 " --> pdb=" O PRO a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 72 Processing helix chain 'a' and resid 72 through 79 Processing helix chain 'a' and resid 81 through 90 Processing helix chain 'a' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU a 96 " --> pdb=" O ASP a 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 53 removed outlier: 3.747A pdb=" N ALA b 46 " --> pdb=" O PRO b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 72 Processing helix chain 'b' and resid 72 through 79 Processing helix chain 'b' and resid 81 through 90 Processing helix chain 'b' and resid 90 through 99 removed outlier: 3.543A pdb=" N GLU b 96 " --> pdb=" O ASP b 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 401 Processing helix chain 'B' and resid 429 through 444 Processing helix chain 'B' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG B 682 " --> pdb=" O TYR B 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 401 Processing helix chain 'C' and resid 429 through 444 Processing helix chain 'C' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG C 682 " --> pdb=" O TYR C 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 401 Processing helix chain 'D' and resid 429 through 444 Processing helix chain 'D' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG D 682 " --> pdb=" O TYR D 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 401 Processing helix chain 'E' and resid 429 through 444 Processing helix chain 'E' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG E 682 " --> pdb=" O TYR E 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 401 Processing helix chain 'F' and resid 429 through 444 Processing helix chain 'F' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG F 682 " --> pdb=" O TYR F 679 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 401 Processing helix chain 'G' and resid 429 through 444 Processing helix chain 'G' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG G 682 " --> pdb=" O TYR G 679 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 401 Processing helix chain 'H' and resid 429 through 444 Processing helix chain 'H' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG H 682 " --> pdb=" O TYR H 679 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 401 Processing helix chain 'I' and resid 429 through 444 Processing helix chain 'I' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG I 682 " --> pdb=" O TYR I 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 401 Processing helix chain 'J' and resid 429 through 444 Processing helix chain 'J' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG J 682 " --> pdb=" O TYR J 679 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 401 Processing helix chain 'K' and resid 429 through 444 Processing helix chain 'K' and resid 679 through 683 removed outlier: 3.931A pdb=" N ARG K 682 " --> pdb=" O TYR K 679 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 401 Processing helix chain 'L' and resid 429 through 444 Processing helix chain 'L' and resid 679 through 683 removed outlier: 3.931A pdb=" N ARG L 682 " --> pdb=" O TYR L 679 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 401 Processing helix chain 'M' and resid 429 through 444 Processing helix chain 'M' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG M 682 " --> pdb=" O TYR M 679 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 401 Processing helix chain 'N' and resid 429 through 444 Processing helix chain 'N' and resid 679 through 683 removed outlier: 3.930A pdb=" N ARG N 682 " --> pdb=" O TYR N 679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 383 Processing sheet with id=AA2, first strand: chain 'A' and resid 414 through 418 Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 476 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 480 through 483 current: chain 'A' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 541 through 567 current: chain 'A' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 685 through 705 current: chain 'B' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 480 through 483 current: chain 'B' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 541 through 567 current: chain 'B' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 685 through 705 current: chain 'C' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 480 through 483 current: chain 'C' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 541 through 567 current: chain 'C' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 685 through 705 current: chain 'D' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 480 through 483 current: chain 'D' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 541 through 567 current: chain 'D' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 685 through 705 current: chain 'E' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 480 through 483 current: chain 'E' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 541 through 567 current: chain 'E' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 685 through 705 current: chain 'F' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 480 through 483 current: chain 'F' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 541 through 567 current: chain 'F' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 685 through 705 current: chain 'G' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 480 through 483 current: chain 'G' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 541 through 567 current: chain 'G' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 685 through 705 current: chain 'H' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 480 through 483 current: chain 'H' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 541 through 567 current: chain 'H' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 685 through 705 current: chain 'I' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 480 through 483 current: chain 'I' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 541 through 567 current: chain 'I' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 685 through 705 current: chain 'J' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 480 through 483 current: chain 'J' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 541 through 567 current: chain 'J' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 685 through 705 current: chain 'K' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 480 through 483 current: chain 'K' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 541 through 567 current: chain 'K' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 685 through 705 current: chain 'L' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 480 through 483 current: chain 'L' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 541 through 567 current: chain 'L' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 685 through 705 current: chain 'M' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 480 through 483 current: chain 'M' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 541 through 567 current: chain 'M' and resid 685 through 705 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 685 through 705 current: chain 'N' and resid 480 through 483 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 480 through 483 current: chain 'N' and resid 541 through 567 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 541 through 567 current: chain 'N' and resid 685 through 705 Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA5, first strand: chain 'A' and resid 498 through 499 Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA7, first strand: chain 'A' and resid 572 through 580 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 613 through 622 current: chain 'A' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 613 through 622 current: chain 'B' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 613 through 622 current: chain 'C' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 613 through 622 current: chain 'D' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 613 through 622 current: chain 'E' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 613 through 622 current: chain 'F' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 613 through 622 current: chain 'G' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 613 through 622 current: chain 'H' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 613 through 622 current: chain 'I' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 613 through 622 current: chain 'J' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 613 through 622 current: chain 'K' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 613 through 622 current: chain 'L' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 613 through 622 current: chain 'M' and resid 637 through 649 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 613 through 622 current: chain 'N' and resid 637 through 649 Processing sheet with id=AA8, first strand: chain 'B' and resid 414 through 418 Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 492 Processing sheet with id=AB1, first strand: chain 'B' and resid 498 through 499 Processing sheet with id=AB2, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AB3, first strand: chain 'C' and resid 414 through 418 Processing sheet with id=AB4, first strand: chain 'C' and resid 490 through 492 Processing sheet with id=AB5, first strand: chain 'C' and resid 498 through 499 Processing sheet with id=AB6, first strand: chain 'C' and resid 510 through 511 Processing sheet with id=AB7, first strand: chain 'D' and resid 414 through 418 Processing sheet with id=AB8, first strand: chain 'D' and resid 490 through 492 Processing sheet with id=AB9, first strand: chain 'D' and resid 498 through 499 Processing sheet with id=AC1, first strand: chain 'D' and resid 510 through 511 Processing sheet with id=AC2, first strand: chain 'E' and resid 414 through 418 Processing sheet with id=AC3, first strand: chain 'E' and resid 490 through 492 Processing sheet with id=AC4, first strand: chain 'E' and resid 498 through 499 Processing sheet with id=AC5, first strand: chain 'E' and resid 510 through 511 Processing sheet with id=AC6, first strand: chain 'F' and resid 414 through 418 Processing sheet with id=AC7, first strand: chain 'F' and resid 490 through 492 Processing sheet with id=AC8, first strand: chain 'F' and resid 498 through 499 Processing sheet with id=AC9, first strand: chain 'F' and resid 510 through 511 Processing sheet with id=AD1, first strand: chain 'G' and resid 414 through 418 Processing sheet with id=AD2, first strand: chain 'G' and resid 490 through 492 Processing sheet with id=AD3, first strand: chain 'G' and resid 498 through 499 Processing sheet with id=AD4, first strand: chain 'G' and resid 510 through 511 Processing sheet with id=AD5, first strand: chain 'H' and resid 414 through 418 Processing sheet with id=AD6, first strand: chain 'H' and resid 490 through 492 Processing sheet with id=AD7, first strand: chain 'H' and resid 498 through 499 Processing sheet with id=AD8, first strand: chain 'H' and resid 510 through 511 Processing sheet with id=AD9, first strand: chain 'I' and resid 414 through 418 Processing sheet with id=AE1, first strand: chain 'I' and resid 490 through 492 Processing sheet with id=AE2, first strand: chain 'I' and resid 498 through 499 Processing sheet with id=AE3, first strand: chain 'I' and resid 510 through 511 Processing sheet with id=AE4, first strand: chain 'J' and resid 414 through 418 Processing sheet with id=AE5, first strand: chain 'J' and resid 490 through 492 Processing sheet with id=AE6, first strand: chain 'J' and resid 498 through 499 Processing sheet with id=AE7, first strand: chain 'J' and resid 510 through 511 Processing sheet with id=AE8, first strand: chain 'K' and resid 414 through 418 Processing sheet with id=AE9, first strand: chain 'K' and resid 490 through 492 Processing sheet with id=AF1, first strand: chain 'K' and resid 498 through 499 Processing sheet with id=AF2, first strand: chain 'K' and resid 510 through 511 Processing sheet with id=AF3, first strand: chain 'L' and resid 414 through 418 Processing sheet with id=AF4, first strand: chain 'L' and resid 490 through 492 Processing sheet with id=AF5, first strand: chain 'L' and resid 498 through 499 Processing sheet with id=AF6, first strand: chain 'L' and resid 510 through 511 Processing sheet with id=AF7, first strand: chain 'M' and resid 414 through 418 Processing sheet with id=AF8, first strand: chain 'M' and resid 490 through 492 Processing sheet with id=AF9, first strand: chain 'M' and resid 498 through 499 Processing sheet with id=AG1, first strand: chain 'M' and resid 510 through 511 Processing sheet with id=AG2, first strand: chain 'N' and resid 490 through 492 Processing sheet with id=AG3, first strand: chain 'N' and resid 498 through 499 Processing sheet with id=AG4, first strand: chain 'N' and resid 510 through 511 1492 hydrogen bonds defined for protein. 4017 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: 7.77 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7261 1.32 - 1.45: 9756 1.45 - 1.57: 24801 1.57 - 1.70: 28 1.70 - 1.82: 252 Bond restraints: 42098 Sorted by residual: bond pdb=" CA CYS Q 104 " pdb=" C CYS Q 104 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.20e-02 6.94e+03 1.53e+01 bond pdb=" CA CYS U 104 " pdb=" C CYS U 104 " ideal model delta sigma weight residual 1.522 1.476 0.047 1.20e-02 6.94e+03 1.51e+01 bond pdb=" CA CYS X 104 " pdb=" C CYS X 104 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.20e-02 6.94e+03 1.50e+01 bond pdb=" CA CYS O 104 " pdb=" C CYS O 104 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.20e-02 6.94e+03 1.50e+01 bond pdb=" CA CYS Y 104 " pdb=" C CYS Y 104 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.20e-02 6.94e+03 1.48e+01 ... (remaining 42093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 55967 2.38 - 4.75: 761 4.75 - 7.13: 154 7.13 - 9.51: 0 9.51 - 11.89: 14 Bond angle restraints: 56896 Sorted by residual: angle pdb=" CB MET B 497 " pdb=" CG MET B 497 " pdb=" SD MET B 497 " ideal model delta sigma weight residual 112.70 124.59 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB MET H 497 " pdb=" CG MET H 497 " pdb=" SD MET H 497 " ideal model delta sigma weight residual 112.70 124.59 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB MET J 497 " pdb=" CG MET J 497 " pdb=" SD MET J 497 " ideal model delta sigma weight residual 112.70 124.57 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB MET N 497 " pdb=" CG MET N 497 " pdb=" SD MET N 497 " ideal model delta sigma weight residual 112.70 124.57 -11.87 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CB MET K 497 " pdb=" CG MET K 497 " pdb=" SD MET K 497 " ideal model delta sigma weight residual 112.70 124.56 -11.86 3.00e+00 1.11e-01 1.56e+01 ... (remaining 56891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 22606 17.11 - 34.23: 2230 34.23 - 51.34: 658 51.34 - 68.46: 308 68.46 - 85.57: 84 Dihedral angle restraints: 25886 sinusoidal: 10598 harmonic: 15288 Sorted by residual: dihedral pdb=" CB CYS S 101 " pdb=" SG CYS S 101 " pdb=" SG CYS S 104 " pdb=" CB CYS S 104 " ideal model delta sinusoidal sigma weight residual -86.00 -116.33 30.33 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CB CYS a 101 " pdb=" SG CYS a 101 " pdb=" SG CYS a 104 " pdb=" CB CYS a 104 " ideal model delta sinusoidal sigma weight residual -86.00 -116.30 30.30 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CB CYS b 101 " pdb=" SG CYS b 101 " pdb=" SG CYS b 104 " pdb=" CB CYS b 104 " ideal model delta sinusoidal sigma weight residual -86.00 -116.29 30.29 1 1.00e+01 1.00e-02 1.31e+01 ... (remaining 25883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4672 0.048 - 0.096: 1333 0.096 - 0.144: 533 0.144 - 0.191: 7 0.191 - 0.239: 35 Chirality restraints: 6580 Sorted by residual: chirality pdb=" CA THR V 105 " pdb=" N THR V 105 " pdb=" C THR V 105 " pdb=" CB THR V 105 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA THR P 105 " pdb=" N THR P 105 " pdb=" C THR P 105 " pdb=" CB THR P 105 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA THR Q 105 " pdb=" N THR Q 105 " pdb=" C THR Q 105 " pdb=" CB THR Q 105 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 6577 not shown) Planarity restraints: 7322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 73 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO R 74 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO R 74 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 74 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU b 73 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO b 74 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO b 74 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO b 74 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU S 73 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO S 74 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO S 74 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 74 " 0.030 5.00e-02 4.00e+02 ... (remaining 7319 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 10955 2.82 - 3.34: 35657 3.34 - 3.86: 72598 3.86 - 4.38: 87194 4.38 - 4.90: 148529 Nonbonded interactions: 354933 Sorted by model distance: nonbonded pdb=" OD2 ASP B 418 " pdb=" OG1 THR B 421 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP M 418 " pdb=" OG1 THR M 421 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP F 418 " pdb=" OG1 THR F 421 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP G 418 " pdb=" OG1 THR G 421 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP E 418 " pdb=" OG1 THR E 421 " model vdw 2.295 3.040 ... (remaining 354928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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: 14.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 32.380 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 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 : 0.004 0.047 42126 Z= 0.221 Angle : 0.715 11.887 56952 Z= 0.386 Chirality : 0.051 0.239 6580 Planarity : 0.005 0.053 7322 Dihedral : 17.173 85.571 16002 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.04 % Allowed : 21.97 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.11), residues: 5278 helix: -0.55 (0.12), residues: 1148 sheet: 0.41 (0.10), residues: 2142 loop : -0.79 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 432 TYR 0.009 0.001 TYR K 679 PHE 0.007 0.001 PHE B 699 TRP 0.010 0.001 TRP H 471 HIS 0.001 0.001 HIS J 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.22 (42098) covalent geometry : angle 0.71359 / 0.39 (56896) SS BOND : bond 0.00148 / 0.10 ( 28) SS BOND : angle 1.51515 / 1.07 ( 56) hydrogen bonds : bond 0.10842 / 7.28 ( 1492) hydrogen bonds : angle 6.51055 / 4.48 ( 4017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 707 time to evaluate : 1.631 Fit side-chains REVERT: A 378 ARG cc_start: 0.7395 (mtm110) cc_final: 0.6753 (ttm170) REVERT: A 552 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8524 (tttm) REVERT: A 665 SER cc_start: 0.9121 (t) cc_final: 0.8919 (p) REVERT: A 693 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8543 (ttmm) REVERT: A 705 MET cc_start: 0.8196 (mmm) cc_final: 0.7848 (mmt) REVERT: O 95 LYS cc_start: 0.7285 (mmtt) cc_final: 0.6590 (tttt) REVERT: P 95 LYS cc_start: 0.7318 (mmtt) cc_final: 0.6554 (tttt) REVERT: R 95 LYS cc_start: 0.7356 (mmtt) cc_final: 0.6687 (tttt) REVERT: S 95 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6576 (tttt) REVERT: T 95 LYS cc_start: 0.7476 (mmtt) cc_final: 0.6712 (tttt) REVERT: U 95 LYS cc_start: 0.7286 (mmtt) cc_final: 0.6517 (tttt) REVERT: V 95 LYS cc_start: 0.7480 (mmtt) cc_final: 0.6645 (tttt) REVERT: W 95 LYS cc_start: 0.7355 (mmtt) cc_final: 0.6679 (tttt) REVERT: X 95 LYS cc_start: 0.7482 (mmtt) cc_final: 0.6754 (tttm) REVERT: X 109 TYR cc_start: 0.6396 (t80) cc_final: 0.6131 (t80) REVERT: Y 95 LYS cc_start: 0.7434 (mmtt) cc_final: 0.6648 (tttt) REVERT: Z 95 LYS cc_start: 0.7450 (mmtt) cc_final: 0.6614 (tttt) REVERT: a 95 LYS cc_start: 0.7540 (mmtt) cc_final: 0.6919 (tttt) REVERT: b 95 LYS cc_start: 0.7477 (mmtt) cc_final: 0.6854 (tttt) REVERT: b 109 TYR cc_start: 0.6303 (t80) cc_final: 0.6015 (t80) REVERT: B 394 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7936 (mttt) REVERT: B 552 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8501 (tttm) REVERT: C 388 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7801 (mtmm) REVERT: C 394 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7963 (mttt) REVERT: C 526 LYS cc_start: 0.8544 (ptmt) cc_final: 0.8305 (pttt) REVERT: C 552 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8535 (tttm) REVERT: C 693 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8676 (ttpt) REVERT: D 378 ARG cc_start: 0.7643 (mtm110) cc_final: 0.6942 (ttm170) REVERT: D 451 MET cc_start: 0.8930 (tpp) cc_final: 0.8654 (tpp) REVERT: D 492 LYS cc_start: 0.7692 (ttpp) cc_final: 0.7190 (ptmm) REVERT: D 552 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8553 (tttm) REVERT: D 693 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8506 (ttmm) REVERT: E 388 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7673 (mtpt) REVERT: E 492 LYS cc_start: 0.7539 (ttpp) cc_final: 0.7300 (ptmm) REVERT: E 552 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8535 (tttm) REVERT: F 515 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7405 (mtpm) REVERT: F 552 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8520 (tttm) REVERT: F 665 SER cc_start: 0.9195 (t) cc_final: 0.8995 (p) REVERT: G 492 LYS cc_start: 0.7578 (ttpp) cc_final: 0.7230 (ptmm) REVERT: G 515 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7452 (mtpm) REVERT: G 526 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8345 (pttt) REVERT: G 552 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8491 (tttm) REVERT: G 693 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8652 (ttmm) REVERT: G 705 MET cc_start: 0.8144 (mmm) cc_final: 0.7884 (mmt) REVERT: H 378 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6758 (ttm170) REVERT: H 552 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8532 (tttm) REVERT: H 665 SER cc_start: 0.9136 (t) cc_final: 0.8929 (p) REVERT: H 693 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8553 (ttmm) REVERT: H 705 MET cc_start: 0.8233 (mmm) cc_final: 0.7870 (mmt) REVERT: I 394 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7915 (mttt) REVERT: I 552 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8503 (tttm) REVERT: I 705 MET cc_start: 0.8150 (mmm) cc_final: 0.7754 (mmt) REVERT: J 394 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7927 (mttt) REVERT: J 526 LYS cc_start: 0.8531 (ptmt) cc_final: 0.8288 (pttt) REVERT: J 552 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8543 (tttm) REVERT: J 693 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8677 (ttpt) REVERT: K 378 ARG cc_start: 0.7628 (mtm110) cc_final: 0.6920 (ttm170) REVERT: K 451 MET cc_start: 0.8936 (tpp) cc_final: 0.8627 (tpp) REVERT: K 492 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7163 (ptmm) REVERT: K 552 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8564 (tttm) REVERT: K 693 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8487 (ttmm) REVERT: K 705 MET cc_start: 0.8184 (mmm) cc_final: 0.7947 (mmm) REVERT: L 388 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7687 (mtpt) REVERT: L 492 LYS cc_start: 0.7541 (ttpp) cc_final: 0.7337 (ptmm) REVERT: L 552 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8539 (tttm) REVERT: M 515 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7412 (mtpm) REVERT: M 526 LYS cc_start: 0.8630 (ptmt) cc_final: 0.8426 (pttt) REVERT: M 552 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8523 (tttm) REVERT: M 665 SER cc_start: 0.9197 (t) cc_final: 0.8990 (p) REVERT: N 492 LYS cc_start: 0.7566 (ttpp) cc_final: 0.7225 (ptmm) REVERT: N 515 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7450 (mtpm) REVERT: N 526 LYS cc_start: 0.8587 (ptmt) cc_final: 0.8347 (pttt) REVERT: N 552 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8486 (tttm) REVERT: N 693 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8652 (ttmm) outliers start: 2 outliers final: 0 residues processed: 709 average time/residue: 0.8180 time to fit residues: 689.8780 Evaluate side-chains 523 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 0.0980 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 0.0570 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 ASN A 643 ASN S 87 GLN Z 87 GLN B 488 ASN B 643 ASN C 488 ASN D 488 ASN D 643 ASN E 488 ASN E 643 ASN F 488 ASN F 643 ASN G 488 ASN G 643 ASN H 488 ASN H 643 ASN I 488 ASN I 643 ASN J 488 ASN K 488 ASN K 643 ASN L 488 ASN L 643 ASN M 488 ASN M 643 ASN N 488 ASN N 643 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.096785 restraints weight = 45958.658| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.34 r_work: 0.2913 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9212 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 42126 Z= 0.154 Angle : 0.569 7.754 56952 Z= 0.287 Chirality : 0.047 0.136 6580 Planarity : 0.005 0.034 7322 Dihedral : 9.557 76.018 6328 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.71 % Allowed : 19.23 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.11), residues: 5278 helix: 1.41 (0.15), residues: 1134 sheet: 0.59 (0.11), residues: 2100 loop : -0.84 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 703 TYR 0.008 0.001 TYR B 463 PHE 0.020 0.002 PHE B 673 TRP 0.010 0.002 TRP K 471 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (42098) covalent geometry : angle 0.56817 / 0.29 (56896) SS BOND : bond 0.00082 / 0.05 ( 28) SS BOND : angle 1.07873 / 0.76 ( 56) hydrogen bonds : bond 0.03256 / 2.25 ( 1492) hydrogen bonds : angle 5.28634 / 3.64 ( 4017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 560 time to evaluate : 1.655 Fit side-chains REVERT: A 378 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7187 (ttm170) REVERT: A 492 LYS cc_start: 0.8026 (ptmt) cc_final: 0.7704 (ptmm) REVERT: A 693 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8713 (ttmm) REVERT: O 95 LYS cc_start: 0.7342 (mmtt) cc_final: 0.6701 (tttt) REVERT: P 95 LYS cc_start: 0.7454 (mmtt) cc_final: 0.6809 (tttt) REVERT: Q 95 LYS cc_start: 0.7269 (mmtt) cc_final: 0.6800 (tttt) REVERT: R 95 LYS cc_start: 0.7370 (mmtt) cc_final: 0.6770 (tttt) REVERT: S 95 LYS cc_start: 0.7318 (mmtt) cc_final: 0.6728 (tttt) REVERT: T 95 LYS cc_start: 0.7500 (mmtt) cc_final: 0.6929 (tttt) REVERT: U 95 LYS cc_start: 0.7404 (mmtt) cc_final: 0.6757 (tttt) REVERT: V 95 LYS cc_start: 0.7451 (mmtt) cc_final: 0.6761 (tttt) REVERT: W 95 LYS cc_start: 0.7455 (mmtt) cc_final: 0.6887 (tttt) REVERT: X 95 LYS cc_start: 0.7544 (mmtt) cc_final: 0.6968 (tttm) REVERT: Y 95 LYS cc_start: 0.7478 (mmtt) cc_final: 0.6808 (tttt) REVERT: Z 95 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6812 (tttt) REVERT: a 95 LYS cc_start: 0.7457 (mmtt) cc_final: 0.6964 (tttt) REVERT: b 95 LYS cc_start: 0.7525 (mmtt) cc_final: 0.6966 (tttt) REVERT: B 378 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7247 (ttm170) REVERT: B 646 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9072 (pt) REVERT: C 378 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7235 (ttm170) REVERT: C 394 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8427 (mttt) REVERT: C 693 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8788 (ttpt) REVERT: D 378 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7339 (ttm170) REVERT: D 515 LYS cc_start: 0.8512 (mptp) cc_final: 0.7972 (mtpt) REVERT: D 693 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8594 (ttmm) REVERT: E 378 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7231 (ttm170) REVERT: E 388 LYS cc_start: 0.8328 (mtmm) cc_final: 0.7960 (mtpt) REVERT: F 431 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: F 515 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8006 (mtpt) REVERT: G 431 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: G 515 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8003 (mtpt) REVERT: G 526 LYS cc_start: 0.8660 (ptmt) cc_final: 0.8420 (pttt) REVERT: G 693 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8763 (ttmm) REVERT: G 705 MET cc_start: 0.8344 (mmm) cc_final: 0.8129 (mmt) REVERT: H 378 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7198 (ttm170) REVERT: H 492 LYS cc_start: 0.8034 (ptmt) cc_final: 0.7706 (ptmm) REVERT: H 526 LYS cc_start: 0.8760 (ptmt) cc_final: 0.8459 (ptmm) REVERT: H 693 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8729 (ttmm) REVERT: I 378 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7246 (ttm170) REVERT: I 646 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9056 (pt) REVERT: J 378 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: J 539 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8189 (t0) REVERT: J 693 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8790 (ttpt) REVERT: K 378 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7343 (ttm170) REVERT: K 451 MET cc_start: 0.8973 (tpp) cc_final: 0.8721 (tpp) REVERT: K 515 LYS cc_start: 0.8514 (mptp) cc_final: 0.7976 (mtpt) REVERT: K 693 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8602 (ttmm) REVERT: L 378 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7207 (ttm170) REVERT: L 388 LYS cc_start: 0.8361 (mtmm) cc_final: 0.7983 (mtpt) REVERT: M 431 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7821 (pt0) REVERT: M 515 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7999 (mtpt) REVERT: N 431 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: N 515 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8000 (mtpt) REVERT: N 526 LYS cc_start: 0.8663 (ptmt) cc_final: 0.8430 (pttt) REVERT: N 693 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8768 (ttmm) outliers start: 165 outliers final: 51 residues processed: 669 average time/residue: 0.8117 time to fit residues: 652.1926 Evaluate side-chains 572 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 502 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain G residue 693 LYS Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 652 GLU Chi-restraints excluded: chain I residue 693 LYS Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain J residue 693 LYS Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 623 ASP Chi-restraints excluded: chain K residue 652 GLU Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 431 GLU Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain M residue 431 GLU Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 652 GLU Chi-restraints excluded: chain N residue 693 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 459 optimal weight: 0.8980 chunk 464 optimal weight: 0.2980 chunk 373 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 470 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 408 optimal weight: 8.9990 chunk 345 optimal weight: 3.9990 chunk 407 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN B 643 ASN D 643 ASN E 643 ASN F 643 ASN G 643 ASN H 643 ASN I 643 ASN J 385 ASN K 643 ASN L 643 ASN M 643 ASN N 643 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097657 restraints weight = 45966.215| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.34 r_work: 0.2929 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9201 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 42126 Z= 0.110 Angle : 0.523 8.290 56952 Z= 0.262 Chirality : 0.046 0.134 6580 Planarity : 0.004 0.040 7322 Dihedral : 9.136 70.907 6328 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.13 % Allowed : 19.45 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.12), residues: 5278 helix: 2.15 (0.16), residues: 1148 sheet: 0.53 (0.11), residues: 2142 loop : -0.69 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 703 TYR 0.006 0.001 TYR D 463 PHE 0.013 0.001 PHE B 673 TRP 0.006 0.001 TRP K 471 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (42098) covalent geometry : angle 0.52247 / 0.26 (56896) SS BOND : bond 0.00114 / 0.08 ( 28) SS BOND : angle 0.62996 / 0.45 ( 56) hydrogen bonds : bond 0.03056 / 2.11 ( 1492) hydrogen bonds : angle 5.05076 / 3.48 ( 4017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 558 time to evaluate : 1.573 Fit side-chains REVERT: A 378 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7210 (ttm170) REVERT: A 492 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7809 (ptmm) REVERT: A 693 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8712 (ttmm) REVERT: O 95 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6795 (tttt) REVERT: P 95 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6810 (tttt) REVERT: Q 95 LYS cc_start: 0.7375 (mmtt) cc_final: 0.6941 (tttt) REVERT: R 95 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6770 (tttt) REVERT: S 95 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6758 (tttt) REVERT: T 95 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6953 (tttt) REVERT: U 95 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6800 (tttt) REVERT: V 95 LYS cc_start: 0.7530 (mmtt) cc_final: 0.6869 (tttt) REVERT: W 95 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6908 (tttt) REVERT: X 95 LYS cc_start: 0.7519 (mmtt) cc_final: 0.6988 (tttt) REVERT: Y 95 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6796 (tttt) REVERT: Z 95 LYS cc_start: 0.7376 (mmtt) cc_final: 0.6812 (tttt) REVERT: a 95 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7007 (tttt) REVERT: b 95 LYS cc_start: 0.7468 (mmtt) cc_final: 0.6956 (tttt) REVERT: B 378 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7258 (ttm170) REVERT: B 646 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9038 (pt) REVERT: C 378 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7244 (ttm170) REVERT: C 394 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8436 (mttt) REVERT: C 574 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9025 (tp) REVERT: C 630 MET cc_start: 0.8640 (mmm) cc_final: 0.8437 (tpp) REVERT: D 378 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7365 (ttm170) REVERT: D 574 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9045 (tp) REVERT: D 693 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8591 (ttmm) REVERT: E 378 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7239 (ttm170) REVERT: E 388 LYS cc_start: 0.8276 (mtmm) cc_final: 0.7922 (mtpt) REVERT: E 515 LYS cc_start: 0.8512 (mptp) cc_final: 0.8066 (mtpt) REVERT: F 515 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8003 (mtpt) REVERT: G 431 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: G 515 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8009 (mtpt) REVERT: G 526 LYS cc_start: 0.8631 (ptmt) cc_final: 0.8341 (pttt) REVERT: G 693 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8756 (ttmm) REVERT: G 705 MET cc_start: 0.8331 (mmm) cc_final: 0.8123 (mmt) REVERT: H 378 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7226 (ttm170) REVERT: H 492 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7819 (ptmm) REVERT: H 693 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8723 (ttmm) REVERT: I 378 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7261 (ttm170) REVERT: I 646 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9034 (pt) REVERT: J 378 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7242 (ttm170) REVERT: J 394 LYS cc_start: 0.8668 (mttp) cc_final: 0.8457 (mttt) REVERT: J 539 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8194 (t0) REVERT: J 574 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9047 (tp) REVERT: J 630 MET cc_start: 0.8634 (mmm) cc_final: 0.8428 (tpp) REVERT: K 378 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7375 (ttm170) REVERT: K 515 LYS cc_start: 0.8510 (mptp) cc_final: 0.7981 (mtpt) REVERT: K 574 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9051 (tp) REVERT: K 693 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8605 (ttmm) REVERT: L 378 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: L 388 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7952 (mtpt) REVERT: L 515 LYS cc_start: 0.8451 (mptp) cc_final: 0.8019 (mtpt) REVERT: M 515 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8002 (mtpt) REVERT: N 431 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: N 515 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7994 (mtpt) REVERT: N 693 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8754 (ttmm) outliers start: 184 outliers final: 49 residues processed: 672 average time/residue: 0.7995 time to fit residues: 647.9761 Evaluate side-chains 586 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 508 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain U residue 95 LYS Chi-restraints excluded: chain W residue 95 LYS Chi-restraints excluded: chain Y residue 95 LYS Chi-restraints excluded: chain a residue 95 LYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 575 LEU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 492 LYS Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 431 GLU Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 575 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 183 optimal weight: 0.2980 chunk 526 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 518 optimal weight: 2.9990 chunk 416 optimal weight: 3.9990 chunk 408 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 GLN A 643 ASN B 546 GLN B 643 ASN C 546 GLN D 546 GLN D 643 ASN E 546 GLN E 643 ASN F 546 GLN F 643 ASN G 546 GLN G 643 ASN H 643 ASN I 546 GLN I 643 ASN J 546 GLN K 546 GLN K 643 ASN L 546 GLN L 643 ASN M 546 GLN M 643 ASN N 546 GLN N 643 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.094442 restraints weight = 46159.911| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.34 r_work: 0.2811 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 42126 Z= 0.197 Angle : 0.586 8.744 56952 Z= 0.290 Chirality : 0.047 0.132 6580 Planarity : 0.005 0.041 7322 Dihedral : 9.595 69.219 6328 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.22 % Allowed : 19.38 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.11), residues: 5278 helix: 1.99 (0.16), residues: 1134 sheet: 0.60 (0.11), residues: 2100 loop : -0.73 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 703 TYR 0.009 0.001 TYR B 463 PHE 0.019 0.002 PHE I 673 TRP 0.010 0.002 TRP K 471 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (42098) covalent geometry : angle 0.58595 / 0.29 (56896) SS BOND : bond 0.00195 / 0.12 ( 28) SS BOND : angle 0.73310 / 0.51 ( 56) hydrogen bonds : bond 0.03330 / 2.29 ( 1492) hydrogen bonds : angle 5.11696 / 3.52 ( 4017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 514 time to evaluate : 1.667 Fit side-chains REVERT: A 378 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7127 (ttm170) REVERT: A 492 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7767 (ptmm) REVERT: A 515 LYS cc_start: 0.8285 (mptp) cc_final: 0.7800 (mtpt) REVERT: A 574 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9163 (tp) REVERT: A 693 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8637 (ttmm) REVERT: O 95 LYS cc_start: 0.7305 (mmtt) cc_final: 0.6632 (tttt) REVERT: P 95 LYS cc_start: 0.7369 (mmtt) cc_final: 0.6674 (tttt) REVERT: Q 95 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6729 (tttt) REVERT: R 95 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6571 (tttt) REVERT: S 95 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6581 (tttt) REVERT: T 84 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8079 (mtmp) REVERT: T 95 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6740 (tttt) REVERT: U 95 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6581 (tttt) REVERT: V 95 LYS cc_start: 0.7286 (mmtt) cc_final: 0.6618 (tttt) REVERT: W 95 LYS cc_start: 0.7415 (mmtt) cc_final: 0.6760 (tttt) REVERT: X 36 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.5670 (tmt) REVERT: X 95 LYS cc_start: 0.7406 (mmtt) cc_final: 0.6708 (tttt) REVERT: Y 95 LYS cc_start: 0.7312 (mmtt) cc_final: 0.6616 (tttt) REVERT: Z 95 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6631 (tttt) REVERT: a 95 LYS cc_start: 0.7378 (mmtt) cc_final: 0.6785 (tttt) REVERT: b 95 LYS cc_start: 0.7317 (mmtt) cc_final: 0.6665 (tttt) REVERT: B 378 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7143 (ttm170) REVERT: B 515 LYS cc_start: 0.8326 (mptp) cc_final: 0.7745 (mtpt) REVERT: B 646 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9071 (pt) REVERT: C 378 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7141 (ttm170) REVERT: C 574 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9096 (tp) REVERT: C 669 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: D 378 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7228 (ttm170) REVERT: D 515 LYS cc_start: 0.8333 (mptp) cc_final: 0.7807 (mtpt) REVERT: D 574 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9120 (tp) REVERT: D 693 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8582 (ttmm) REVERT: E 378 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7092 (ttm170) REVERT: E 388 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7699 (mtpt) REVERT: E 492 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7355 (ptmm) REVERT: E 515 LYS cc_start: 0.8375 (mptp) cc_final: 0.7880 (mtpt) REVERT: F 431 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: F 515 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7862 (mtpt) REVERT: F 669 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: G 431 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: G 492 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7505 (ptmm) REVERT: G 515 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7889 (mtpt) REVERT: G 693 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8721 (ttmm) REVERT: G 705 MET cc_start: 0.8426 (mmm) cc_final: 0.8108 (mmt) REVERT: H 378 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7120 (ttm170) REVERT: H 492 LYS cc_start: 0.8146 (ptmt) cc_final: 0.7720 (ptmm) REVERT: H 515 LYS cc_start: 0.8279 (mptp) cc_final: 0.7796 (mtpt) REVERT: H 574 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9154 (tp) REVERT: H 693 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8639 (ttmm) REVERT: I 378 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7138 (ttm170) REVERT: I 497 MET cc_start: 0.6705 (mmm) cc_final: 0.6430 (tpt) REVERT: I 515 LYS cc_start: 0.8315 (mptp) cc_final: 0.7738 (mtpt) REVERT: I 646 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9067 (pt) REVERT: J 378 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7137 (ttm170) REVERT: J 394 LYS cc_start: 0.8548 (mttp) cc_final: 0.8300 (mttt) REVERT: J 574 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9084 (tp) REVERT: K 378 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7227 (ttm170) REVERT: K 515 LYS cc_start: 0.8419 (mptp) cc_final: 0.7868 (mtpt) REVERT: K 574 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9120 (tp) REVERT: K 693 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8584 (ttmm) REVERT: L 378 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7087 (ttm170) REVERT: L 388 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7715 (mtpt) REVERT: L 492 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7532 (ptmm) REVERT: L 515 LYS cc_start: 0.8383 (mptp) cc_final: 0.7889 (mtpt) REVERT: M 431 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: M 515 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7877 (mtpt) REVERT: M 669 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: N 431 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: N 492 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7576 (ptmm) REVERT: N 515 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7886 (mtpt) REVERT: N 693 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8724 (ttmm) outliers start: 188 outliers final: 64 residues processed: 640 average time/residue: 0.8291 time to fit residues: 636.1034 Evaluate side-chains 594 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 501 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Z residue 95 LYS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 526 LYS Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 652 GLU Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain F residue 669 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 431 GLU Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain M residue 431 GLU Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain M residue 669 GLU Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 526 LYS Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 652 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 404 optimal weight: 3.9990 chunk 343 optimal weight: 4.9990 chunk 455 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 355 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 492 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN Z 87 GLN B 643 ASN D 643 ASN E 643 ASN F 643 ASN G 643 ASN H 546 GLN H 643 ASN I 643 ASN K 643 ASN L 643 ASN M 643 ASN N 643 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.097091 restraints weight = 46286.064| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.34 r_work: 0.2879 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 42126 Z= 0.135 Angle : 0.531 9.519 56952 Z= 0.264 Chirality : 0.046 0.132 6580 Planarity : 0.004 0.041 7322 Dihedral : 9.249 65.266 6328 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.82 % Allowed : 20.01 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.12), residues: 5278 helix: 2.21 (0.16), residues: 1134 sheet: 0.66 (0.10), residues: 2240 loop : -0.53 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 703 TYR 0.009 0.001 TYR J 582 PHE 0.013 0.001 PHE B 673 TRP 0.007 0.001 TRP K 471 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (42098) covalent geometry : angle 0.53073 / 0.26 (56896) SS BOND : bond 0.00162 / 0.10 ( 28) SS BOND : angle 0.51033 / 0.36 ( 56) hydrogen bonds : bond 0.03050 / 2.10 ( 1492) hydrogen bonds : angle 4.97537 / 3.43 ( 4017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 540 time to evaluate : 1.655 Fit side-chains REVERT: A 378 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7223 (ttm170) REVERT: A 492 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7865 (ptmm) REVERT: A 515 LYS cc_start: 0.8332 (mptp) cc_final: 0.7871 (mtpt) REVERT: A 693 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8688 (ttmm) REVERT: O 95 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6812 (tttt) REVERT: P 95 LYS cc_start: 0.7450 (mmtt) cc_final: 0.6848 (tttt) REVERT: Q 95 LYS cc_start: 0.7443 (mmtt) cc_final: 0.6850 (tttm) REVERT: R 95 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6739 (tttt) REVERT: S 95 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6735 (tttm) REVERT: T 95 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6889 (tttt) REVERT: U 95 LYS cc_start: 0.7414 (mmtt) cc_final: 0.6790 (tttt) REVERT: V 95 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6799 (tttt) REVERT: W 95 LYS cc_start: 0.7519 (mmtt) cc_final: 0.6942 (tttt) REVERT: X 95 LYS cc_start: 0.7506 (mmtt) cc_final: 0.6838 (tttt) REVERT: Y 95 LYS cc_start: 0.7431 (mmtt) cc_final: 0.6817 (tttt) REVERT: Z 95 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6773 (tttt) REVERT: a 95 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6906 (tttt) REVERT: b 95 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6771 (tttt) REVERT: B 378 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7233 (ttm170) REVERT: B 515 LYS cc_start: 0.8411 (mptp) cc_final: 0.7855 (mtpt) REVERT: B 646 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9100 (pt) REVERT: B 705 MET cc_start: 0.8033 (mmt) cc_final: 0.7710 (mmt) REVERT: C 378 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7218 (ttm170) REVERT: C 431 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: D 378 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7315 (ttm170) REVERT: D 515 LYS cc_start: 0.8423 (mptp) cc_final: 0.7939 (mtpt) REVERT: D 574 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9057 (tp) REVERT: D 582 TYR cc_start: 0.8418 (p90) cc_final: 0.8218 (p90) REVERT: D 693 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8651 (ttmm) REVERT: D 695 GLU cc_start: 0.8009 (tp30) cc_final: 0.7698 (tm-30) REVERT: E 378 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7206 (ttm170) REVERT: E 388 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7785 (mtpt) REVERT: E 401 SER cc_start: 0.7518 (p) cc_final: 0.7274 (m) REVERT: E 515 LYS cc_start: 0.8450 (mptp) cc_final: 0.7994 (mtpt) REVERT: F 394 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8399 (mttt) REVERT: F 515 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7941 (mtpt) REVERT: F 695 GLU cc_start: 0.8084 (tp30) cc_final: 0.7776 (tm-30) REVERT: G 401 SER cc_start: 0.7692 (p) cc_final: 0.7351 (m) REVERT: G 431 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: G 515 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7995 (mtpt) REVERT: G 693 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8731 (ttmm) REVERT: G 705 MET cc_start: 0.8441 (mmm) cc_final: 0.8175 (mmt) REVERT: H 378 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: H 492 LYS cc_start: 0.8202 (ptmt) cc_final: 0.7829 (ptmm) REVERT: H 515 LYS cc_start: 0.8324 (mptp) cc_final: 0.7864 (mtpt) REVERT: H 693 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8687 (ttmm) REVERT: I 378 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7227 (ttm170) REVERT: I 497 MET cc_start: 0.6784 (mmm) cc_final: 0.6571 (tpt) REVERT: I 515 LYS cc_start: 0.8415 (mptp) cc_final: 0.7864 (mtpt) REVERT: I 646 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9101 (pt) REVERT: J 378 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7211 (ttm170) REVERT: J 388 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7760 (mtpt) REVERT: J 394 LYS cc_start: 0.8634 (mttp) cc_final: 0.8398 (mttt) REVERT: J 431 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: K 378 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7332 (ttm170) REVERT: K 515 LYS cc_start: 0.8467 (mptp) cc_final: 0.7996 (mtpt) REVERT: K 574 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9052 (tp) REVERT: K 582 TYR cc_start: 0.8408 (p90) cc_final: 0.8205 (p90) REVERT: K 693 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8653 (ttmm) REVERT: K 695 GLU cc_start: 0.8012 (tp30) cc_final: 0.7738 (tm-30) REVERT: L 378 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: L 388 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7809 (mtpt) REVERT: L 401 SER cc_start: 0.7516 (p) cc_final: 0.7265 (m) REVERT: L 515 LYS cc_start: 0.8440 (mptp) cc_final: 0.7969 (mtpt) REVERT: M 394 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8366 (mttt) REVERT: M 497 MET cc_start: 0.6893 (mmm) cc_final: 0.6677 (tpt) REVERT: M 515 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7939 (mtpt) REVERT: M 695 GLU cc_start: 0.8096 (tp30) cc_final: 0.7784 (tm-30) REVERT: N 394 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8380 (mttt) REVERT: N 431 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: N 515 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7982 (mtpt) REVERT: N 693 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8718 (ttmm) outliers start: 170 outliers final: 57 residues processed: 656 average time/residue: 0.8086 time to fit residues: 638.4031 Evaluate side-chains 599 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 515 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain Z residue 95 LYS Chi-restraints excluded: chain a residue 95 LYS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 652 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 652 GLU Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 431 GLU Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 630 MET Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain M residue 394 LYS Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain N residue 394 LYS Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 526 LYS Chi-restraints excluded: chain N residue 652 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 111 optimal weight: 0.7980 chunk 435 optimal weight: 0.0570 chunk 15 optimal weight: 3.9990 chunk 228 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 473 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 495 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN B 643 ASN D 643 ASN E 643 ASN F 643 ASN G 643 ASN H 643 ASN I 643 ASN K 643 ASN L 643 ASN M 643 ASN N 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.096098 restraints weight = 46653.966| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.34 r_work: 0.2848 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 42126 Z= 0.163 Angle : 0.544 9.813 56952 Z= 0.272 Chirality : 0.047 0.131 6580 Planarity : 0.004 0.038 7322 Dihedral : 9.406 62.699 6328 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.80 % Allowed : 20.22 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.12), residues: 5278 helix: 2.25 (0.16), residues: 1120 sheet: 0.64 (0.10), residues: 2226 loop : -0.56 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 703 TYR 0.009 0.001 TYR C 582 PHE 0.016 0.002 PHE F 673 TRP 0.008 0.001 TRP D 471 HIS 0.001 0.000 HIS F 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (42098) covalent geometry : angle 0.54447 / 0.27 (56896) SS BOND : bond 0.00188 / 0.12 ( 28) SS BOND : angle 0.53745 / 0.38 ( 56) hydrogen bonds : bond 0.03151 / 2.17 ( 1492) hydrogen bonds : angle 5.01041 / 3.45 ( 4017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 529 time to evaluate : 1.615 Fit side-chains REVERT: A 378 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: A 492 LYS cc_start: 0.8168 (ptmt) cc_final: 0.7820 (ptmm) REVERT: A 497 MET cc_start: 0.6797 (mmm) cc_final: 0.6530 (tpt) REVERT: A 515 LYS cc_start: 0.8282 (mptp) cc_final: 0.7798 (mtpt) REVERT: A 550 MET cc_start: 0.9169 (tmt) cc_final: 0.8949 (tmt) REVERT: A 574 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9112 (tp) REVERT: A 693 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8667 (ttmm) REVERT: O 95 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6686 (tttt) REVERT: P 95 LYS cc_start: 0.7429 (mmtt) cc_final: 0.6809 (tttt) REVERT: Q 95 LYS cc_start: 0.7457 (mmtt) cc_final: 0.6816 (tttm) REVERT: R 95 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6681 (tttt) REVERT: S 95 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6671 (tttt) REVERT: T 95 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6800 (tttt) REVERT: U 95 LYS cc_start: 0.7377 (mmtt) cc_final: 0.6723 (tttt) REVERT: V 95 LYS cc_start: 0.7353 (mmtt) cc_final: 0.6755 (tttt) REVERT: W 95 LYS cc_start: 0.7444 (mmtt) cc_final: 0.6845 (tttt) REVERT: X 36 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.5748 (tmt) REVERT: X 95 LYS cc_start: 0.7455 (mmtt) cc_final: 0.6774 (tttm) REVERT: Y 95 LYS cc_start: 0.7389 (mmtt) cc_final: 0.6732 (tttt) REVERT: Z 95 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6699 (tttt) REVERT: a 95 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6861 (tttt) REVERT: b 95 LYS cc_start: 0.7349 (mmtt) cc_final: 0.6705 (tttt) REVERT: B 378 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7197 (ttm170) REVERT: B 515 LYS cc_start: 0.8380 (mptp) cc_final: 0.7824 (mtpt) REVERT: B 532 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9141 (tp) REVERT: B 646 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9103 (pt) REVERT: B 695 GLU cc_start: 0.8028 (tp30) cc_final: 0.7743 (tm-30) REVERT: C 378 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7197 (ttm170) REVERT: C 388 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7708 (mtpt) REVERT: C 431 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7842 (pt0) REVERT: C 669 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: D 378 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7275 (ttm170) REVERT: D 394 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8391 (mttp) REVERT: D 515 LYS cc_start: 0.8397 (mptp) cc_final: 0.7909 (mtpt) REVERT: D 574 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9059 (tp) REVERT: D 582 TYR cc_start: 0.8416 (p90) cc_final: 0.8191 (p90) REVERT: D 693 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8644 (ttmm) REVERT: D 695 GLU cc_start: 0.8049 (tp30) cc_final: 0.7764 (tm-30) REVERT: E 378 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7164 (ttm170) REVERT: E 388 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7726 (mtpt) REVERT: E 401 SER cc_start: 0.7449 (p) cc_final: 0.7204 (m) REVERT: E 515 LYS cc_start: 0.8431 (mptp) cc_final: 0.7950 (mtpt) REVERT: F 394 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8330 (mttt) REVERT: F 431 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7890 (pt0) REVERT: F 515 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7909 (mtpt) REVERT: F 669 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8501 (mt-10) REVERT: F 695 GLU cc_start: 0.8082 (tp30) cc_final: 0.7811 (tm-30) REVERT: G 401 SER cc_start: 0.7669 (p) cc_final: 0.7331 (m) REVERT: G 431 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: G 492 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7688 (ptmm) REVERT: G 515 LYS cc_start: 0.8390 (mmtt) cc_final: 0.7953 (mtpt) REVERT: G 693 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8720 (ttmm) REVERT: G 705 MET cc_start: 0.8424 (mmm) cc_final: 0.8137 (mmt) REVERT: H 378 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7218 (ttm170) REVERT: H 492 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7813 (ptmm) REVERT: H 497 MET cc_start: 0.6762 (mmm) cc_final: 0.6501 (tpt) REVERT: H 515 LYS cc_start: 0.8277 (mptp) cc_final: 0.7800 (mtpt) REVERT: H 550 MET cc_start: 0.9174 (tmt) cc_final: 0.8958 (tmt) REVERT: H 693 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8676 (ttmm) REVERT: I 378 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7177 (ttm170) REVERT: I 515 LYS cc_start: 0.8384 (mptp) cc_final: 0.7836 (mtpt) REVERT: I 532 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9132 (tp) REVERT: I 557 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8045 (mm-30) REVERT: I 646 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9119 (pt) REVERT: I 695 GLU cc_start: 0.7999 (tp30) cc_final: 0.7707 (tm-30) REVERT: J 378 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7184 (ttm170) REVERT: J 388 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7691 (mtpt) REVERT: J 394 LYS cc_start: 0.8623 (mttp) cc_final: 0.8382 (mttt) REVERT: J 431 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: K 378 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7273 (ttm170) REVERT: K 394 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8389 (mttp) REVERT: K 515 LYS cc_start: 0.8445 (mptp) cc_final: 0.7934 (mtpt) REVERT: K 574 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9054 (tp) REVERT: K 582 TYR cc_start: 0.8406 (p90) cc_final: 0.8179 (p90) REVERT: K 693 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8640 (ttmm) REVERT: K 695 GLU cc_start: 0.8073 (tp30) cc_final: 0.7769 (tm-30) REVERT: L 378 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7160 (ttm170) REVERT: L 388 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7747 (mtpt) REVERT: L 401 SER cc_start: 0.7448 (p) cc_final: 0.7203 (m) REVERT: L 515 LYS cc_start: 0.8429 (mptp) cc_final: 0.7945 (mtpt) REVERT: M 394 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8329 (mttt) REVERT: M 431 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: M 497 MET cc_start: 0.6800 (mmm) cc_final: 0.6553 (tpt) REVERT: M 515 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7898 (mtpt) REVERT: M 526 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8590 (ptpt) REVERT: M 669 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8479 (mt-10) REVERT: M 695 GLU cc_start: 0.8099 (tp30) cc_final: 0.7820 (tm-30) REVERT: N 394 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8307 (mttt) REVERT: N 401 SER cc_start: 0.7603 (p) cc_final: 0.7231 (m) REVERT: N 431 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: N 492 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7731 (ptmm) REVERT: N 515 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7940 (mtpt) REVERT: N 693 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8706 (ttmm) outliers start: 169 outliers final: 63 residues processed: 640 average time/residue: 0.8273 time to fit residues: 635.6654 Evaluate side-chains 613 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 510 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Z residue 95 LYS Chi-restraints excluded: chain a residue 95 LYS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 652 GLU Chi-restraints excluded: chain F residue 388 LYS Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain F residue 669 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 532 ILE Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 388 LYS Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 394 LYS Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 574 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 431 GLU Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 630 MET Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain M residue 388 LYS Chi-restraints excluded: chain M residue 394 LYS Chi-restraints excluded: chain M residue 431 GLU Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 526 LYS Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain M residue 669 GLU Chi-restraints excluded: chain N residue 394 LYS Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 526 LYS Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 652 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 273 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 223 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 334 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 337 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 447 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN B 643 ASN D 643 ASN E 643 ASN F 643 ASN G 643 ASN H 643 ASN I 643 ASN K 643 ASN L 643 ASN M 643 ASN N 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097713 restraints weight = 46324.500| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.34 r_work: 0.2853 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 42126 Z= 0.116 Angle : 0.512 10.776 56952 Z= 0.256 Chirality : 0.046 0.132 6580 Planarity : 0.004 0.040 7322 Dihedral : 9.092 59.776 6328 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.68 % Allowed : 20.42 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.12), residues: 5278 helix: 2.37 (0.16), residues: 1134 sheet: 0.66 (0.10), residues: 2240 loop : -0.45 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 703 TYR 0.009 0.001 TYR J 582 PHE 0.011 0.001 PHE F 673 TRP 0.006 0.001 TRP A 471 HIS 0.001 0.000 HIS M 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (42098) covalent geometry : angle 0.51200 / 0.26 (56896) SS BOND : bond 0.00175 / 0.11 ( 28) SS BOND : angle 0.43320 / 0.30 ( 56) hydrogen bonds : bond 0.02927 / 2.02 ( 1492) hydrogen bonds : angle 4.91220 / 3.39 ( 4017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 531 time to evaluate : 1.668 Fit side-chains REVERT: A 378 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7093 (ttm170) REVERT: A 492 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7767 (ptmm) REVERT: A 497 MET cc_start: 0.6748 (mmm) cc_final: 0.6489 (tpt) REVERT: A 515 LYS cc_start: 0.8167 (mptp) cc_final: 0.7687 (mtpt) REVERT: A 550 MET cc_start: 0.9145 (tmt) cc_final: 0.8919 (tmt) REVERT: A 693 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8606 (ttmm) REVERT: A 695 GLU cc_start: 0.8051 (tp30) cc_final: 0.7751 (tm-30) REVERT: O 95 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6586 (tttt) REVERT: P 95 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6670 (tttt) REVERT: Q 95 LYS cc_start: 0.7291 (mmtt) cc_final: 0.6632 (tttm) REVERT: R 95 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6570 (tttt) REVERT: S 95 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6481 (tttm) REVERT: T 36 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.5933 (tmt) REVERT: T 95 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6631 (tttt) REVERT: U 95 LYS cc_start: 0.7304 (mmtt) cc_final: 0.6587 (tttt) REVERT: V 95 LYS cc_start: 0.7178 (mmtt) cc_final: 0.6539 (tttt) REVERT: W 95 LYS cc_start: 0.7289 (mmtt) cc_final: 0.6653 (tttt) REVERT: X 36 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.5698 (tmt) REVERT: X 95 LYS cc_start: 0.7312 (mmtt) cc_final: 0.6637 (tttt) REVERT: Y 95 LYS cc_start: 0.7324 (mmtt) cc_final: 0.6638 (tttt) REVERT: Z 95 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6529 (tttt) REVERT: a 95 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6674 (tttt) REVERT: b 95 LYS cc_start: 0.7194 (mmtt) cc_final: 0.6522 (tttt) REVERT: B 378 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7076 (ttm170) REVERT: B 515 LYS cc_start: 0.8271 (mptp) cc_final: 0.7682 (mtpt) REVERT: B 557 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7910 (mm-30) REVERT: B 646 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9072 (pt) REVERT: B 695 GLU cc_start: 0.7963 (tp30) cc_final: 0.7682 (tm-30) REVERT: C 378 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7085 (ttm170) REVERT: C 388 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7487 (mtpt) REVERT: C 431 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: C 669 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: D 378 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7130 (ttm170) REVERT: D 515 LYS cc_start: 0.8281 (mptp) cc_final: 0.7760 (mtpt) REVERT: D 630 MET cc_start: 0.8748 (mmt) cc_final: 0.8399 (mmt) REVERT: D 693 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8577 (ttmm) REVERT: D 695 GLU cc_start: 0.8043 (tp30) cc_final: 0.7731 (tm-30) REVERT: E 378 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7034 (ttm170) REVERT: E 388 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7534 (mtpt) REVERT: E 401 SER cc_start: 0.7288 (p) cc_final: 0.7057 (m) REVERT: E 515 LYS cc_start: 0.8320 (mptp) cc_final: 0.7830 (mtpt) REVERT: F 394 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8235 (mttt) REVERT: F 431 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: F 515 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7746 (mtpt) REVERT: F 669 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: F 695 GLU cc_start: 0.8057 (tp30) cc_final: 0.7790 (tm-30) REVERT: G 401 SER cc_start: 0.7382 (p) cc_final: 0.7010 (m) REVERT: G 431 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: G 515 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7798 (mtpt) REVERT: G 532 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9042 (tp) REVERT: G 693 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8651 (ttmm) REVERT: G 705 MET cc_start: 0.8362 (mmm) cc_final: 0.8052 (mmt) REVERT: H 378 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7102 (ttm170) REVERT: H 492 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7781 (ptmm) REVERT: H 497 MET cc_start: 0.6709 (mmm) cc_final: 0.6458 (tpt) REVERT: H 515 LYS cc_start: 0.8161 (mptp) cc_final: 0.7676 (mtpt) REVERT: H 550 MET cc_start: 0.9151 (tmt) cc_final: 0.8925 (tmt) REVERT: H 557 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7916 (mm-30) REVERT: H 693 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8614 (ttmm) REVERT: H 695 GLU cc_start: 0.8047 (tp30) cc_final: 0.7756 (tm-30) REVERT: I 378 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7057 (ttm170) REVERT: I 515 LYS cc_start: 0.8283 (mptp) cc_final: 0.7705 (mtpt) REVERT: I 532 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9082 (tp) REVERT: I 557 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7952 (mm-30) REVERT: I 646 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9090 (pt) REVERT: I 695 GLU cc_start: 0.7972 (tp30) cc_final: 0.7686 (tm-30) REVERT: J 378 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7068 (ttm170) REVERT: J 388 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7482 (mtpt) REVERT: J 394 LYS cc_start: 0.8485 (mttp) cc_final: 0.8248 (mttt) REVERT: J 431 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: K 378 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7156 (ttm170) REVERT: K 515 LYS cc_start: 0.8334 (mptp) cc_final: 0.7828 (mtpt) REVERT: K 582 TYR cc_start: 0.8344 (p90) cc_final: 0.8143 (p90) REVERT: K 693 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8569 (ttmm) REVERT: K 695 GLU cc_start: 0.8081 (tp30) cc_final: 0.7777 (tm-30) REVERT: L 378 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7024 (ttm170) REVERT: L 388 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7571 (mtpt) REVERT: L 401 SER cc_start: 0.7298 (p) cc_final: 0.7065 (m) REVERT: L 515 LYS cc_start: 0.8318 (mptp) cc_final: 0.7826 (mtpt) REVERT: M 394 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8206 (mttt) REVERT: M 431 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7842 (pt0) REVERT: M 497 MET cc_start: 0.6735 (mmm) cc_final: 0.6496 (tpt) REVERT: M 515 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7776 (mtpt) REVERT: M 669 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8465 (mt-10) REVERT: M 695 GLU cc_start: 0.8044 (tp30) cc_final: 0.7793 (tm-30) REVERT: N 394 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8237 (mttt) REVERT: N 401 SER cc_start: 0.7371 (p) cc_final: 0.6991 (m) REVERT: N 431 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: N 515 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7785 (mtpt) REVERT: N 532 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9036 (tp) REVERT: N 693 LYS cc_start: 0.8940 (ttmt) cc_final: 0.8636 (ttmm) outliers start: 164 outliers final: 58 residues processed: 640 average time/residue: 0.8242 time to fit residues: 633.4083 Evaluate side-chains 609 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 512 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 36 MET Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Z residue 95 LYS Chi-restraints excluded: chain a residue 95 LYS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 388 LYS Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain F residue 669 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 492 LYS Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 532 ILE Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 388 LYS Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 388 LYS Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 630 MET Chi-restraints excluded: chain M residue 394 LYS Chi-restraints excluded: chain M residue 431 GLU Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain M residue 669 GLU Chi-restraints excluded: chain N residue 394 LYS Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 532 ILE Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 616 VAL Chi-restraints excluded: chain N residue 652 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 259 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 430 optimal weight: 0.0980 chunk 486 optimal weight: 0.7980 chunk 348 optimal weight: 7.9990 chunk 449 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 522 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 445 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN B 643 ASN D 643 ASN E 643 ASN F 643 ASN G 643 ASN H 643 ASN I 643 ASN K 643 ASN L 643 ASN M 643 ASN N 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.096674 restraints weight = 46459.940| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.34 r_work: 0.2857 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 42126 Z= 0.149 Angle : 0.532 10.177 56952 Z= 0.266 Chirality : 0.046 0.131 6580 Planarity : 0.004 0.041 7322 Dihedral : 9.243 59.897 6328 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.17 % Allowed : 20.78 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.12), residues: 5278 helix: 2.33 (0.16), residues: 1134 sheet: 0.68 (0.10), residues: 2240 loop : -0.46 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 703 TYR 0.015 0.001 TYR D 582 PHE 0.015 0.002 PHE F 673 TRP 0.007 0.001 TRP D 471 HIS 0.001 0.000 HIS F 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (42098) covalent geometry : angle 0.53232 / 0.27 (56896) SS BOND : bond 0.00183 / 0.12 ( 28) SS BOND : angle 0.50559 / 0.35 ( 56) hydrogen bonds : bond 0.03063 / 2.11 ( 1492) hydrogen bonds : angle 4.95731 / 3.42 ( 4017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 520 time to evaluate : 1.684 Fit side-chains REVERT: A 378 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7221 (ttm170) REVERT: A 492 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7864 (ptmm) REVERT: A 497 MET cc_start: 0.6781 (mmm) cc_final: 0.6527 (tpt) REVERT: A 515 LYS cc_start: 0.8287 (mptp) cc_final: 0.7805 (mtpt) REVERT: A 550 MET cc_start: 0.9178 (tmt) cc_final: 0.8889 (tmt) REVERT: A 693 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8677 (ttmm) REVERT: A 695 GLU cc_start: 0.8097 (tp30) cc_final: 0.7803 (tm-30) REVERT: O 95 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6712 (tttt) REVERT: P 95 LYS cc_start: 0.7467 (mmtt) cc_final: 0.6869 (tttt) REVERT: Q 95 LYS cc_start: 0.7463 (mmtt) cc_final: 0.6830 (tttm) REVERT: R 95 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6709 (tttt) REVERT: S 95 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6667 (tttm) REVERT: T 36 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.5899 (tmt) REVERT: T 95 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6849 (tttt) REVERT: U 95 LYS cc_start: 0.7460 (mmtt) cc_final: 0.6799 (tttt) REVERT: V 95 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6754 (tttt) REVERT: W 95 LYS cc_start: 0.7467 (mmtt) cc_final: 0.6872 (tttt) REVERT: X 36 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.5765 (tmt) REVERT: X 95 LYS cc_start: 0.7405 (mmtt) cc_final: 0.6737 (tttm) REVERT: Y 95 LYS cc_start: 0.7473 (mmtt) cc_final: 0.6802 (tttt) REVERT: Z 95 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6728 (tttm) REVERT: a 95 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6831 (tttt) REVERT: b 95 LYS cc_start: 0.7348 (mmtt) cc_final: 0.6723 (tttt) REVERT: B 378 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7208 (ttm170) REVERT: B 515 LYS cc_start: 0.8382 (mptp) cc_final: 0.7828 (mtpt) REVERT: B 557 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8004 (mm-30) REVERT: B 574 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8839 (tp) REVERT: B 646 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9094 (pt) REVERT: B 695 GLU cc_start: 0.8079 (tp30) cc_final: 0.7818 (tm-30) REVERT: C 378 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7222 (ttm170) REVERT: C 388 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7669 (mtpt) REVERT: C 431 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: D 378 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7251 (ttm170) REVERT: D 515 LYS cc_start: 0.8397 (mptp) cc_final: 0.7897 (mtpt) REVERT: D 630 MET cc_start: 0.8801 (mmt) cc_final: 0.8489 (mmt) REVERT: D 693 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8640 (ttmm) REVERT: D 695 GLU cc_start: 0.8110 (tp30) cc_final: 0.7805 (tm-30) REVERT: D 705 MET cc_start: 0.8110 (mmt) cc_final: 0.7860 (mmm) REVERT: E 378 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7182 (ttm170) REVERT: E 388 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7722 (mtpt) REVERT: E 401 SER cc_start: 0.7448 (p) cc_final: 0.7226 (m) REVERT: E 492 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7479 (ptmm) REVERT: E 515 LYS cc_start: 0.8432 (mptp) cc_final: 0.7939 (mtpt) REVERT: F 394 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8341 (mttt) REVERT: F 431 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: F 515 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7889 (mtpt) REVERT: F 574 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9093 (tp) REVERT: F 669 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: F 695 GLU cc_start: 0.8080 (tp30) cc_final: 0.7824 (tm-30) REVERT: G 401 SER cc_start: 0.7556 (p) cc_final: 0.7210 (m) REVERT: G 431 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: G 492 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7617 (ptmm) REVERT: G 515 LYS cc_start: 0.8380 (mmtt) cc_final: 0.7926 (mtpt) REVERT: G 532 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9101 (tp) REVERT: G 693 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8724 (ttmm) REVERT: G 695 GLU cc_start: 0.8372 (tp30) cc_final: 0.8091 (tm-30) REVERT: G 705 MET cc_start: 0.8409 (mmm) cc_final: 0.8129 (mmt) REVERT: H 378 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7228 (ttm170) REVERT: H 492 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7864 (ptmm) REVERT: H 497 MET cc_start: 0.6732 (mmm) cc_final: 0.6485 (tpt) REVERT: H 515 LYS cc_start: 0.8286 (mptp) cc_final: 0.7805 (mtpt) REVERT: H 550 MET cc_start: 0.9181 (tmt) cc_final: 0.8897 (tmt) REVERT: H 693 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8664 (ttmm) REVERT: H 695 GLU cc_start: 0.8071 (tp30) cc_final: 0.7781 (tm-30) REVERT: I 378 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7190 (ttm170) REVERT: I 515 LYS cc_start: 0.8382 (mptp) cc_final: 0.7839 (mtpt) REVERT: I 557 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8040 (mm-30) REVERT: I 574 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8854 (tp) REVERT: I 646 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9113 (pt) REVERT: I 695 GLU cc_start: 0.8060 (tp30) cc_final: 0.7791 (tm-30) REVERT: J 378 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7207 (ttm170) REVERT: J 388 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7656 (mtpt) REVERT: J 394 LYS cc_start: 0.8633 (mttp) cc_final: 0.8396 (mttt) REVERT: J 431 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: K 378 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7258 (ttm170) REVERT: K 515 LYS cc_start: 0.8440 (mptp) cc_final: 0.7927 (mtpt) REVERT: K 693 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8628 (ttmm) REVERT: K 695 GLU cc_start: 0.8089 (tp30) cc_final: 0.7786 (tm-30) REVERT: L 378 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7149 (ttm170) REVERT: L 388 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7747 (mtpt) REVERT: L 401 SER cc_start: 0.7421 (p) cc_final: 0.7199 (m) REVERT: L 492 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7476 (ptmm) REVERT: L 515 LYS cc_start: 0.8431 (mptp) cc_final: 0.7933 (mtpt) REVERT: M 394 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8332 (mttt) REVERT: M 431 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: M 497 MET cc_start: 0.6766 (mmm) cc_final: 0.6508 (tpt) REVERT: M 515 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7903 (mtpt) REVERT: M 574 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9094 (tp) REVERT: M 669 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: M 695 GLU cc_start: 0.8092 (tp30) cc_final: 0.7828 (tm-30) REVERT: N 394 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8357 (mttt) REVERT: N 431 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: N 492 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7719 (ptmm) REVERT: N 515 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7901 (mtpt) REVERT: N 532 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9095 (tp) REVERT: N 693 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8711 (ttmm) REVERT: N 695 GLU cc_start: 0.8385 (tp30) cc_final: 0.8105 (tm-30) outliers start: 141 outliers final: 66 residues processed: 611 average time/residue: 0.8486 time to fit residues: 620.3614 Evaluate side-chains 616 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 512 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 36 MET Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Z residue 95 LYS Chi-restraints excluded: chain a residue 95 LYS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 630 MET Chi-restraints excluded: chain E residue 652 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain F residue 669 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 532 ILE Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 574 ILE Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 630 MET Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 652 GLU Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 388 LYS Chi-restraints excluded: chain L residue 431 GLU Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 630 MET Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain M residue 394 LYS Chi-restraints excluded: chain M residue 431 GLU Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain M residue 669 GLU Chi-restraints excluded: chain N residue 394 LYS Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 532 ILE Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 652 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 188 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 chunk 95 optimal weight: 4.9990 chunk 426 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 402 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN B 643 ASN D 643 ASN E 643 ASN F 643 ASN G 643 ASN H 643 ASN I 643 ASN K 643 ASN L 643 ASN M 643 ASN N 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.097299 restraints weight = 46433.278| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.33 r_work: 0.2867 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9180 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 42126 Z= 0.132 Angle : 0.522 11.064 56952 Z= 0.261 Chirality : 0.046 0.132 6580 Planarity : 0.004 0.041 7322 Dihedral : 9.141 59.322 6328 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.19 % Allowed : 20.89 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 5278 helix: 2.40 (0.16), residues: 1134 sheet: 0.66 (0.10), residues: 2212 loop : -0.41 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 703 TYR 0.013 0.001 TYR K 582 PHE 0.013 0.001 PHE J 673 TRP 0.006 0.001 TRP A 471 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (42098) covalent geometry : angle 0.52166 / 0.26 (56896) SS BOND : bond 0.00171 / 0.11 ( 28) SS BOND : angle 0.42822 / 0.30 ( 56) hydrogen bonds : bond 0.02982 / 2.05 ( 1492) hydrogen bonds : angle 4.92143 / 3.39 ( 4017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 522 time to evaluate : 1.670 Fit side-chains REVERT: A 378 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7236 (ttm170) REVERT: A 492 LYS cc_start: 0.8194 (ptmt) cc_final: 0.7872 (ptmm) REVERT: A 497 MET cc_start: 0.6794 (mmm) cc_final: 0.6551 (tpt) REVERT: A 515 LYS cc_start: 0.8289 (mptp) cc_final: 0.7803 (mtpt) REVERT: A 550 MET cc_start: 0.9188 (tmt) cc_final: 0.8886 (tmt) REVERT: A 574 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9084 (tp) REVERT: A 693 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8676 (ttmm) REVERT: A 695 GLU cc_start: 0.8122 (tp30) cc_final: 0.7822 (tm-30) REVERT: O 95 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6720 (tttt) REVERT: P 95 LYS cc_start: 0.7455 (mmtt) cc_final: 0.6888 (tttt) REVERT: Q 95 LYS cc_start: 0.7459 (mmtt) cc_final: 0.6836 (tttm) REVERT: R 95 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6697 (tttt) REVERT: S 95 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6674 (tttm) REVERT: T 95 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6835 (tttt) REVERT: U 95 LYS cc_start: 0.7451 (mmtt) cc_final: 0.6796 (tttt) REVERT: V 95 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6740 (tttt) REVERT: W 95 LYS cc_start: 0.7450 (mmtt) cc_final: 0.6886 (tttt) REVERT: X 36 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.5765 (tmt) REVERT: X 95 LYS cc_start: 0.7418 (mmtt) cc_final: 0.6790 (tttt) REVERT: Y 95 LYS cc_start: 0.7453 (mmtt) cc_final: 0.6783 (tttt) REVERT: Z 95 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6723 (tttt) REVERT: a 95 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6830 (tttt) REVERT: b 95 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6704 (tttt) REVERT: B 378 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7209 (ttm170) REVERT: B 515 LYS cc_start: 0.8424 (mptp) cc_final: 0.7858 (mtpt) REVERT: B 557 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 646 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9021 (pp) REVERT: B 695 GLU cc_start: 0.8104 (tp30) cc_final: 0.7847 (tm-30) REVERT: C 378 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7210 (ttm170) REVERT: C 388 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7655 (mtpt) REVERT: C 431 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: D 378 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7229 (ttm170) REVERT: D 515 LYS cc_start: 0.8392 (mptp) cc_final: 0.7887 (mtpt) REVERT: D 693 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8631 (ttmm) REVERT: D 695 GLU cc_start: 0.8101 (tp30) cc_final: 0.7870 (tm-30) REVERT: D 705 MET cc_start: 0.8104 (mmt) cc_final: 0.7869 (mmm) REVERT: E 378 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7180 (ttm170) REVERT: E 388 LYS cc_start: 0.8103 (mtmm) cc_final: 0.7698 (mtpt) REVERT: E 401 SER cc_start: 0.7346 (p) cc_final: 0.7130 (m) REVERT: E 492 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7495 (ptmm) REVERT: E 515 LYS cc_start: 0.8470 (mptp) cc_final: 0.7973 (mtpt) REVERT: F 394 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8358 (mttt) REVERT: F 431 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: F 515 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7886 (mtpt) REVERT: F 574 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9079 (tp) REVERT: F 669 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8473 (mt-10) REVERT: F 695 GLU cc_start: 0.8163 (tp30) cc_final: 0.7864 (tm-30) REVERT: G 431 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: G 515 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7914 (mtpt) REVERT: G 532 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9099 (tp) REVERT: G 693 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8724 (ttmm) REVERT: G 695 GLU cc_start: 0.8386 (tp30) cc_final: 0.8101 (tm-30) REVERT: G 705 MET cc_start: 0.8403 (mmm) cc_final: 0.8128 (mmt) REVERT: H 378 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7235 (ttm170) REVERT: H 492 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7864 (ptmm) REVERT: H 497 MET cc_start: 0.6750 (mmm) cc_final: 0.6514 (tpt) REVERT: H 515 LYS cc_start: 0.8296 (mptp) cc_final: 0.7806 (mtpt) REVERT: H 550 MET cc_start: 0.9179 (tmt) cc_final: 0.8881 (tmt) REVERT: H 574 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9045 (tp) REVERT: H 693 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8664 (ttmm) REVERT: H 695 GLU cc_start: 0.8086 (tp30) cc_final: 0.7796 (tm-30) REVERT: I 378 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7199 (ttm170) REVERT: I 515 LYS cc_start: 0.8425 (mptp) cc_final: 0.7871 (mtpt) REVERT: I 557 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7995 (mm-30) REVERT: I 646 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9088 (pt) REVERT: I 695 GLU cc_start: 0.8085 (tp30) cc_final: 0.7827 (tm-30) REVERT: J 378 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7207 (ttm170) REVERT: J 388 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7637 (mtpt) REVERT: J 394 LYS cc_start: 0.8643 (mttp) cc_final: 0.8406 (mttt) REVERT: J 431 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: K 378 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7251 (ttm170) REVERT: K 515 LYS cc_start: 0.8434 (mptp) cc_final: 0.7918 (mtpt) REVERT: K 693 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8622 (ttmm) REVERT: K 695 GLU cc_start: 0.8068 (tp30) cc_final: 0.7836 (tm-30) REVERT: L 378 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7155 (ttm170) REVERT: L 388 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7713 (mtpt) REVERT: L 401 SER cc_start: 0.7338 (p) cc_final: 0.7121 (m) REVERT: L 515 LYS cc_start: 0.8464 (mptp) cc_final: 0.7964 (mtpt) REVERT: M 394 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8327 (mttt) REVERT: M 431 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: M 497 MET cc_start: 0.6743 (mmm) cc_final: 0.6495 (tpt) REVERT: M 515 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7881 (mtpt) REVERT: M 574 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9082 (tp) REVERT: M 669 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: M 695 GLU cc_start: 0.8085 (tp30) cc_final: 0.7823 (tm-30) REVERT: N 394 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8360 (mttt) REVERT: N 431 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: N 515 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7894 (mtpt) REVERT: N 532 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9094 (tp) REVERT: N 693 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8706 (ttmm) REVERT: N 695 GLU cc_start: 0.8392 (tp30) cc_final: 0.8110 (tm-30) outliers start: 142 outliers final: 69 residues processed: 612 average time/residue: 0.8485 time to fit residues: 620.9196 Evaluate side-chains 621 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 514 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Z residue 95 LYS Chi-restraints excluded: chain a residue 95 LYS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 630 MET Chi-restraints excluded: chain E residue 652 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain F residue 669 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 388 LYS Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 532 ILE Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 630 MET Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 388 LYS Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 630 MET Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 652 GLU Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 388 LYS Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 630 MET Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain M residue 388 LYS Chi-restraints excluded: chain M residue 394 LYS Chi-restraints excluded: chain M residue 431 GLU Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain M residue 669 GLU Chi-restraints excluded: chain N residue 394 LYS Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 532 ILE Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 643 ASN Chi-restraints excluded: chain N residue 652 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 348 optimal weight: 7.9990 chunk 459 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 526 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 389 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 448 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN B 643 ASN D 643 ASN E 643 ASN F 643 ASN G 643 ASN H 643 ASN I 643 ASN K 643 ASN L 643 ASN M 643 ASN N 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096818 restraints weight = 46362.299| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.33 r_work: 0.2860 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 42126 Z= 0.153 Angle : 0.535 10.718 56952 Z= 0.267 Chirality : 0.046 0.131 6580 Planarity : 0.004 0.042 7322 Dihedral : 9.223 59.237 6328 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.85 % Allowed : 21.25 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.12), residues: 5278 helix: 2.36 (0.16), residues: 1134 sheet: 0.66 (0.10), residues: 2212 loop : -0.44 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 703 TYR 0.015 0.001 TYR D 582 PHE 0.014 0.002 PHE I 673 TRP 0.007 0.001 TRP D 471 HIS 0.001 0.000 HIS J 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (42098) covalent geometry : angle 0.53531 / 0.27 (56896) SS BOND : bond 0.00179 / 0.11 ( 28) SS BOND : angle 0.44376 / 0.31 ( 56) hydrogen bonds : bond 0.03062 / 2.11 ( 1492) hydrogen bonds : angle 4.95151 / 3.41 ( 4017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10556 Ramachandran restraints generated. 5278 Oldfield, 0 Emsley, 5278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 515 time to evaluate : 1.987 Fit side-chains REVERT: A 378 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7250 (ttm170) REVERT: A 492 LYS cc_start: 0.8193 (ptmt) cc_final: 0.7871 (ptmm) REVERT: A 497 MET cc_start: 0.6784 (mmm) cc_final: 0.6541 (tpt) REVERT: A 515 LYS cc_start: 0.8297 (mptp) cc_final: 0.7807 (mtpt) REVERT: A 550 MET cc_start: 0.9189 (tmt) cc_final: 0.8935 (tmt) REVERT: A 574 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9084 (tp) REVERT: A 693 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8664 (ttmm) REVERT: A 695 GLU cc_start: 0.8133 (tp30) cc_final: 0.7830 (tm-30) REVERT: O 95 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6711 (tttt) REVERT: P 95 LYS cc_start: 0.7492 (mmtt) cc_final: 0.6894 (tttt) REVERT: Q 95 LYS cc_start: 0.7435 (mmtt) cc_final: 0.6797 (tttm) REVERT: R 95 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6705 (tttt) REVERT: S 95 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6666 (tttm) REVERT: T 95 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6849 (tttt) REVERT: U 95 LYS cc_start: 0.7470 (mmtt) cc_final: 0.6801 (tttt) REVERT: V 95 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6750 (tttt) REVERT: W 95 LYS cc_start: 0.7483 (mmtt) cc_final: 0.6883 (tttt) REVERT: X 36 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.5807 (tmt) REVERT: X 95 LYS cc_start: 0.7405 (mmtt) cc_final: 0.6730 (tttm) REVERT: Y 95 LYS cc_start: 0.7482 (mmtt) cc_final: 0.6800 (tttt) REVERT: Z 95 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6718 (tttm) REVERT: a 95 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6825 (tttt) REVERT: b 95 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6707 (tttt) REVERT: B 378 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7211 (ttm170) REVERT: B 515 LYS cc_start: 0.8417 (mptp) cc_final: 0.7850 (mtpt) REVERT: B 646 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9110 (pt) REVERT: B 695 GLU cc_start: 0.8105 (tp30) cc_final: 0.7846 (tm-30) REVERT: C 378 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: C 388 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7659 (mtpt) REVERT: C 431 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: D 378 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7231 (ttm170) REVERT: D 515 LYS cc_start: 0.8395 (mptp) cc_final: 0.7894 (mtpt) REVERT: D 693 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8633 (ttmm) REVERT: D 695 GLU cc_start: 0.8105 (tp30) cc_final: 0.7877 (tm-30) REVERT: D 705 MET cc_start: 0.8099 (mmt) cc_final: 0.7856 (mmm) REVERT: E 378 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7172 (ttm170) REVERT: E 388 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7717 (mtpt) REVERT: E 401 SER cc_start: 0.7367 (p) cc_final: 0.7151 (m) REVERT: E 492 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7512 (ptmm) REVERT: E 515 LYS cc_start: 0.8469 (mptp) cc_final: 0.7971 (mtpt) REVERT: F 394 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8341 (mttt) REVERT: F 431 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: F 515 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7893 (mtpt) REVERT: F 574 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9099 (tp) REVERT: F 669 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (mt-10) REVERT: F 695 GLU cc_start: 0.8161 (tp30) cc_final: 0.7882 (tm-30) REVERT: G 431 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: G 492 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7634 (ptmm) REVERT: G 515 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7916 (mtpt) REVERT: G 532 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9100 (tp) REVERT: G 693 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8723 (ttmm) REVERT: G 695 GLU cc_start: 0.8396 (tp30) cc_final: 0.8088 (tm-30) REVERT: G 705 MET cc_start: 0.8407 (mmm) cc_final: 0.8132 (mmt) REVERT: H 378 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7251 (ttm170) REVERT: H 492 LYS cc_start: 0.8191 (ptmt) cc_final: 0.7859 (ptmm) REVERT: H 497 MET cc_start: 0.6758 (mmm) cc_final: 0.6516 (tpt) REVERT: H 515 LYS cc_start: 0.8301 (mptp) cc_final: 0.7807 (mtpt) REVERT: H 550 MET cc_start: 0.9177 (tmt) cc_final: 0.8928 (tmt) REVERT: H 574 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9060 (tp) REVERT: H 693 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8664 (ttmm) REVERT: H 695 GLU cc_start: 0.8106 (tp30) cc_final: 0.7812 (tm-30) REVERT: I 378 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7203 (ttm170) REVERT: I 515 LYS cc_start: 0.8427 (mptp) cc_final: 0.7868 (mtpt) REVERT: I 557 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8007 (mm-30) REVERT: I 646 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9095 (pt) REVERT: I 695 GLU cc_start: 0.8107 (tp30) cc_final: 0.7847 (tm-30) REVERT: J 378 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7207 (ttm170) REVERT: J 388 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7644 (mtpt) REVERT: J 394 LYS cc_start: 0.8650 (mttp) cc_final: 0.8414 (mttt) REVERT: J 431 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: K 378 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7249 (ttm170) REVERT: K 515 LYS cc_start: 0.8436 (mptp) cc_final: 0.7921 (mtpt) REVERT: K 693 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8617 (ttmm) REVERT: K 695 GLU cc_start: 0.8106 (tp30) cc_final: 0.7878 (tm-30) REVERT: L 378 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7159 (ttm170) REVERT: L 388 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7739 (mtpt) REVERT: L 401 SER cc_start: 0.7341 (p) cc_final: 0.7123 (m) REVERT: L 492 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7520 (ptmm) REVERT: L 515 LYS cc_start: 0.8472 (mptp) cc_final: 0.7971 (mtpt) REVERT: M 394 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8324 (mttt) REVERT: M 431 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: M 497 MET cc_start: 0.6734 (mmm) cc_final: 0.6484 (tpt) REVERT: M 515 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7889 (mtpt) REVERT: M 574 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9099 (tp) REVERT: M 669 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: M 695 GLU cc_start: 0.8088 (tp30) cc_final: 0.7826 (tm-30) REVERT: N 394 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8367 (mttt) REVERT: N 431 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: N 515 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7896 (mtpt) REVERT: N 532 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9097 (tp) REVERT: N 693 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8710 (ttmm) REVERT: N 695 GLU cc_start: 0.8406 (tp30) cc_final: 0.8100 (tm-30) outliers start: 127 outliers final: 63 residues processed: 596 average time/residue: 0.8408 time to fit residues: 599.6581 Evaluate side-chains 608 residues out of total 4452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 508 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Z residue 95 LYS Chi-restraints excluded: chain a residue 95 LYS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain E residue 388 LYS Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 630 MET Chi-restraints excluded: chain E residue 652 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 616 VAL Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 652 GLU Chi-restraints excluded: chain F residue 669 GLU Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 514 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 542 ILE Chi-restraints excluded: chain G residue 652 GLU Chi-restraints excluded: chain H residue 378 ARG Chi-restraints excluded: chain H residue 431 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain H residue 542 ILE Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 648 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 514 SER Chi-restraints excluded: chain I residue 532 ILE Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 646 ILE Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain J residue 378 ARG Chi-restraints excluded: chain J residue 388 LYS Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain J residue 542 ILE Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 630 MET Chi-restraints excluded: chain J residue 648 VAL Chi-restraints excluded: chain J residue 690 THR Chi-restraints excluded: chain K residue 388 LYS Chi-restraints excluded: chain K residue 514 SER Chi-restraints excluded: chain K residue 542 ILE Chi-restraints excluded: chain K residue 652 GLU Chi-restraints excluded: chain K residue 690 THR Chi-restraints excluded: chain L residue 378 ARG Chi-restraints excluded: chain L residue 388 LYS Chi-restraints excluded: chain L residue 431 GLU Chi-restraints excluded: chain L residue 514 SER Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 630 MET Chi-restraints excluded: chain M residue 394 LYS Chi-restraints excluded: chain M residue 431 GLU Chi-restraints excluded: chain M residue 514 SER Chi-restraints excluded: chain M residue 542 ILE Chi-restraints excluded: chain M residue 574 ILE Chi-restraints excluded: chain M residue 616 VAL Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 GLU Chi-restraints excluded: chain M residue 669 GLU Chi-restraints excluded: chain N residue 394 LYS Chi-restraints excluded: chain N residue 431 GLU Chi-restraints excluded: chain N residue 514 SER Chi-restraints excluded: chain N residue 532 ILE Chi-restraints excluded: chain N residue 542 ILE Chi-restraints excluded: chain N residue 652 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 52 optimal weight: 0.0970 chunk 325 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 311 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 523 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN B 643 ASN D 643 ASN E 643 ASN F 643 ASN G 643 ASN H 643 ASN I 643 ASN K 643 ASN L 643 ASN M 643 ASN N 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.097185 restraints weight = 46667.864| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.34 r_work: 0.2865 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 42126 Z= 0.136 Angle : 0.525 10.823 56952 Z= 0.262 Chirality : 0.046 0.131 6580 Planarity : 0.004 0.042 7322 Dihedral : 9.166 59.791 6328 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.81 % Allowed : 21.34 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 5278 helix: 2.40 (0.16), residues: 1134 sheet: 0.66 (0.10), residues: 2212 loop : -0.42 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 703 TYR 0.013 0.001 TYR D 582 PHE 0.013 0.001 PHE I 673 TRP 0.006 0.001 TRP E 471 HIS 0.001 0.000 HIS M 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (42098) covalent geometry : angle 0.52513 / 0.26 (56896) SS BOND : bond 0.00169 / 0.11 ( 28) SS BOND : angle 0.42994 / 0.30 ( 56) hydrogen bonds : bond 0.03004 / 2.07 ( 1492) hydrogen bonds : angle 4.93684 / 3.40 ( 4017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14833.48 seconds wall clock time: 253 minutes 39.47 seconds (15219.47 seconds total)